Tailored oils

ABSTRACT

Recombinant DNA techniques are used to produce oleaginous recombinant cells that produce triglyceride oils having desired fatty acid profiles and regiospecific or stereospecific profiles. Genes manipulated include those encoding stearoyl-ACP desaturase, delta 12 fatty acid desaturase, acyl-ACP thioesterase, ketoacyl-ACP synthase, and lysophosphatidic acid acyltransferase. The oil produced can have enhanced oxidative or thermal stability, or can be useful as a frying oil, shortening, roll-in shortening, tempering fat, cocoa butter replacement, as a lubricant, or as a feedstock for various chemical processes. The fatty acid profile can be enriched in midchain profiles or the oil can be enriched in triglycerides of the saturated-unsaturated-saturated type.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.14/506,491, filed Oct. 3, 2014, which claims the benefit under 35 U.S.C.119(e) of U.S. Provisional Patent Application Nos. 61/887,268, filedOct. 4, 2013; 61/892,399, filed Oct. 17, 2013; 61/895,355, filed Oct.24, 2013; 61/923,327, filed Jan. 3, 2014; and 62/023,109, filed Jul. 10,2014. Each of these applications is incorporated herein by reference inits entirety for all purposes. This application includes subject matterrelated to that disclosed in U.S. Provisional Patent Application No.62/023,112, entitled “Novel Ketoacyl ACP Synthase Genes and UsesThereof,” filed Jul. 10, 2014, which is also hereby incorporated byreference in its entirety for all purposes. In particular, Tables 1, 7and 8 of 62/023,112, and the corresponding sequences identified therein,are hereby incorporated by reference.

REFERENCE TO A SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 28, 2017, isnamed SOLAP059US-SL.txt and is 599,266 bytes in size.

This application includes an electronic sequence listing in a file named“452572-Sequence2.txt”, created on Jan. 20, 2015, and containing 551,031bytes, which is hereby incorporated by reference in its entirety for allpurposes.

FIELD OF THE INVENTION

Embodiments of the present invention relate to oils/fats, fuels, foods,and oleochemicals and their production from cultures of geneticallyengineered cells. Specific embodiments relate to oils with a highcontent of triglycerides bearing fatty acyl groups upon the glycerolbackbone in particular regiospecific patterns, highly stable oils, oilswith high levels of oleic or mid-chain fatty acids, and productsproduced from such oils.

BACKGROUND OF THE INVENTION

PCT Publications WO2008/151149, WO2010/06032, WO2011/150410,WO2011/150411, WO2012/061647, and WO2012/106560 disclose oils andmethods for producing those oils in microbes, including microalgae.These publications also describe the use of such oils to makeoleochemicals and fuels.

Tempering is a process of converting a fat into a desired polymorphicform by manipulation of the temperature of the fat or fat-containingsubstance, commonly used in chocolate making.

Certain enzymes of the fatty acyl-CoA elongation pathway function toextend the length of fatty acyl-CoA molecules. Elongase-complex enzymesextend fatty acyl-CoA molecules in 2 carbon additions, for examplemyristoyl-CoA to palmitoyl-CoA, stearoyl-CoA to arachidyl-CoA, oroleoyl-CoA to eicosanoyl-CoA, eicosanoyl-CoA to erucyl-CoA. In addition,elongase enzymes also extend acyl chain length in 2 carbon increments.KCS enzymes condense acyl-CoA molecules with two carbons frommalonyl-CoA to form beta-ketoacyl-CoA. KCS and elongases may showspecificity for condensing acyl substrates of particular carbon length,modification (such as hydroxylation), or degree of saturation. Forexample, the jojoba (Simmondsia chinensis) beta-ketoacyl-CoA synthasehas been demonstrated to prefer monounsaturated and saturated C18- andC20-CoA substrates to elevate production of erucic acid in transgenicplants (Lassner et al., Plant Cell, 1996, Vol 8(2), pp. 281-292),whereas specific elongase enzymes of Trypanosoma brucei show preferencefor elongating short and midchain saturated CoA substrates (Lee et al.,Cell, 2006, Vol 126(4), pp. 691-9).

The type II fatty acid biosynthetic pathway employs a series ofreactions catalyzed by soluble proteins with intermediates shuttledbetween enzymes as thioesters of acyl carrier protein (ACP). Bycontrast, the type I fatty acid biosynthetic pathway uses a single,large multifunctional polypeptide.

The oleaginous, non-photosynthetic alga, Prototheca moriformis, storescopious amounts of triacylglyceride oil under conditions when thenutritional carbon supply is in excess, but cell division is inhibiteddue to limitation of other essential nutrients. Bulk biosynthesis offatty acids with carbon chain lengths up to C18 occurs in the plastids;fatty acids are then exported to the endoplasmic reticulum where (if itoccurs) elongation past C18 and incorporation into triacylglycerides(TAGs) is believed to occur. Lipids are stored in large cytoplasmicorganelles called lipid bodies until environmental conditions change tofavor growth, whereupon they are mobilized to provide energy and carbonmolecules for anabolic metabolism.

SUMMARY OF THE INVENTION

In accordance with an embodiment, a method includes cultivating arecombinant cell, the cell

-   (i) expressing an exogenous KASI or KASIV gene, optionally encoding    a protein having at least 60, 65, 70, 75, 80, 85, 90, or 95% amino    acid sequence identity to an enzyme encoded by any of SEQ ID NOs:    46-49, and at least one FATB acyl-ACP thioesterase gene optionally    encoding a protein having at least 60, 65, 70, 75, 80, 85, 90, or    95% nucleic acid sequence identity to SEQ ID NOs: 11, 87, 89, 159,    162 or 163;-   (ii) expressing a gene encoding a FATA, FATB, KASI, KASII, LPAAT,    SAD, or FAD2 under the control of a nitrogen-sensitive promoter    having at least 60, 65, 70, 75, 80, 85, 90, or 95% sequence identity    to any of SEQ ID NOs: 129 to 147; or-   (iii) having a knockout or knockdown of a SAD gene, a FAD2 gene, and    a FATA gene, an overexpressing an exogenous C18-preferring FATA    gene, an oleoyl-preferring LPAAT gene, and a KASII gene; and    extracting oil from the cell.

In a related embodiment, the cell is of type (ii) and comprises at leasta second acyl-ACP thioesterase, optionally encoding a protein having atleast 60, 65, 70, 75, 80, 85, 90, or 95% nucleic acid sequence identityto any of SEQ ID NOS:: 11, 87, 89, 159, 162 or 163. The oil can have atleast 30% C10:0 and at least 30% C12:0. The oil can have a viscosity ofless than 30 cS and optionally of 25 cS±20% at 40° C. as measured byASTM D445. The C10:0 and C12:0 fatty acids can be balanced to within20%, 10% or 5%.

In a related embodiment, the cell is of type (iii) and the cell oilcomprises at least 60% stearate-oleate-stearate (SOS). Optionally,theC18-preferring FATA gene encodes a protein with at least 60, 65, 70, 75,80, 85, 90, or 95% amino acid identity to SEQ ID NO: 156, the LPAAT geneencodes a protein with at least 60, 65, 70, 75, 80, 85, 90, or 95% aminoacid identity to SEQ ID NO: 157 and/or the KASII gene encodes a proteinwith at least 60, 65, 70, 75, 80, 85, 90, or 95% amino acid identity toSEQ ID NO 160 or 161.

Optionally, the cell is a microalga, optionally of Trebouxiophyceae, andoptionally of the genus Prototheca.

In a related embodiment, there is an oil, soap, oleochemical, foodstuff,or other oil-derived product produced according to one of theaforementioned methods.

In accordance with an embodiment of the present invention, a methodcomprises cultivating an oleaginous recombinant cell. The cell comprisesan exogenous gene encoding a palmitate ACP-desaturase enzyme active toproduce an oil having a fatty acid profile characterized by a ratio ofpalmitoleic acid to palmitic acid of at least 0.1 and/or palmitoleicacid levels of 0.5% or more, as determined by FAME GC/FID analysis.Optionally, the cell is of an oleaginous recombinant eukaryoticmicroalga.

In related embodiments, the exogenous gene encodes a palmitoyl-ACPdesaturase (PAD) having desaturating activity toward ACP-palmitate.Optionally, the exogenous PAD gene encodes a stearoyl-ACP desaturasevariant having increased activity toward ACP-palmitate. The variant canbe a L118W mutant. The gene can be in operable linkage with a promoter,plastid-targeting transit peptide, and 5′UTR active to express the geneproduct in a eukaryotic oleaginous microalga. The microalga can be ofTrebouxiophyceae, and optionally of the genus Chlorella or Prototheca.Alternately, the microalga has 23 S rRNA with at least 65, 70, 75, 80,85, 90 or 95% nucleotide sequence identity to SEQ ID NO: 76.

Optionally, the fatty acid profile is further characterized by less than3.5% saturated fatty acids. Optionally, the cell is cultivated to atleast 40% oil by dry cell weight. Optionally, the microalga furthercomprises a knockout or knockdown of an endogenous acyl-ACP thioesteraseand/or an exogenous KASII gene. This may reduce the levels of saturatedfatty acids in the oil. For example, the exogenous KASII gene can beinserted into the coding region of the endogenous acyl-ACP thioesterase.Optionally, the inserted KASII gene is inverted in orientation relativeto the endogenous acyl-ACP thioesterase.

In any of these embodiments, the oil can be produced byheterotrophically cultivating the microalga on sucrose and the microalgacomprises an exogenous invertase gene that allows it to metabolize thesucrose.

The oil may be recovered. The recovered oil may be used for frying or asan ingredient in a prepared food. The oil may have a microalga sterolprofile. In a specific embodiment, the microalga sterol profile ischaracterized by an excess of ergosterol over β-sitosterol and/or thepresence of 22, 23-dihydrobrassicasterol, poriferasterol orclionasterol.

In another embodiment, a method comprises cultivating an oleaginouscell, optionally a microalga, so that the cell produces an oil with lessthan 10% palmitic acid, greater than Optionally the cell is a microalgawith FAD and FATA knockouts and expresses an exogenous KASII gene.

In a related embodiment, a method comprises cultivating an oleaginouscell, optionally a microalga, so that the cell produces an oil with afatty acid profile in which: the sum of lauric and myristic acids is atleast 50%; total saturated fatty acids are at least 50% and levels ofcapric and lauric fatty acids are balanced to within 20%; or capric acidis at least 45% and lauric acid is at least 45%. In specific relatedembodiments the sum of lauric and myristic acids is at least 60%, 70% or7%%. Optionally, the cell comprises an exogenous plant FATB gene.

Optionally, the cell comprises an exogenous exogenous KASI or KASIVgene.

The oil may be recovered. The recovered oil may be used for frying or asan ingredient in a prepared food. The oil may have a microalgal sterolprofile. In a specific embodiment, the microalgal sterol profile ischaracterized by an excess of ergosterol over β-sitosterol and/or thepresence of 22, 23-dihydrobrassicasterol, poriferasterol orclionasterol. The oil can be used to make a foodstuff or chemical.

In another embodiment, a method comprises cultivating an oleaginouscell, optionally a microalga, so that the cell produces an oil with afatty acid profile characterized by 10% or less linolenic acid and 20%or more linoleic acid. The cell can comprise an overexpressed KASII geneand a FAD gene replacement. Optionally, the cell comprises an exogenousgene encoding an oleate-specific acyl-ACP thioesterase or a knockout ofone or more FATA alleles, together with an exogenous gene encoding anoleate-specific acyl-ACP thioesterase. The overexpression of the FADgene can be by environmental control of a regulatable promoter. The oilcan be recovered and used to produce a foodstuff or chemicals. The oilmay comprise a microalgal sterol profile.

In another aspect, the present invention provides a method for producinga triglyceride oil, in which the method comprises: (a) cultivating anoleaginous cell under nitrogen-replete conditions, thereby increasingthe number of cells, then; (b) cultivating the cells under nitrogen-poorconditions thereby causing the cells to accumulate triglycerides to atleast 20% by dry cell weight; comprising a FADc (FAD2) allele,optionally a sole allele, under control of a promoter that is activeunder the nitrogen replete conditions and inactive under thenitrogen-starved conditions, the promoter retaining at least half of itsactivity at pH 5.0 as compared to pH 7.0; and (c) obtaining the oil,wherein the oil comprises reduced linoleic acid due to thedownregulation of the FADc gene under the nitrogen-starved conditions.

In some embodiments, the cell is cultivated at a pH of less than 6.5using sucrose in the presence of invertase. In some cases, the invertaseis produced by the cell. In some cases, the invertase is produced froman exogenous gene expressed by the cell.

In some embodiments, the oil obtained has a fatty acid profile with lessthan 3%, 2%, 1%, or 0.5% linoleic acid.

In some embodiments, the cell further comprises a FADc knockout so as toamplify the change in linoleic acid. In some cases, the transcript levelof FADc decreases by a factor of 10 or more between the nitrogen-repleteand nitrogen-starved conditions.

In another aspect, the present invention provides a method for producinga triglyceride cell oil comprising cultivating a recombinant cellcomprising an exogenous FATB gene and an exogenous KASI gene, whereinthe expression of the KASI gene causes the oil to have a shorter chaindistribution relative to a control cell with the FATB gene but withoutthe KASI gene.

In another aspect, the present invention provides a recombinant cellcomprising a FATB acyl-ACP thioesterase gene having at least 75, 80, 85,90, 91, 92, 93, 94, 95, 96, 97, 98, or 88% nucleotide identity to SEQ IDNOs: 90 or 91 or equivalent sequence due to the degeneracy of thegenetic code, or encoding an enzyme having at least 75, 80, 85, 90, 91,92, 93, 94, 95, 96, 97, 98, or 88% amino acid identity to SEQ ID NOs: 90or 91. In some embodiments, the cell produces triglycerides that areshifted in fatty acid profile due to expression of the FATB gene.

In an embodiment of the invention, there is a process for producing anoil. The process includes obtaining a cell oil from a geneticallyengineered microbe, optionally a microalga, and fractionating the celloil to produce a stearin fraction. The stearin fraction can becharacterized by a TAG profile having at least 70% SOS with no more than4% trisaturates and an sn-2 profile characterized by least 90% oleate atthe sn-2 position. Optionally, the microbe is a microalga comprising oneor more of an overexpressed KASII gene, a SAD knockout or knockdown, oran exogenous C18-preferring FATA gene, an exogenous LPAAT, and a FAD2knockout or knockdown. Optionally, the stearin fraction has a maximumheat-flow temperatures or DSC-derived SFC curve that is an essentiallyidentical to the equivalent curve of Kokum butter. The fractionation canbe a two step fractionation performed at a first temperature thatremoves 00S, optionally about 24° C., and a second temperature thatremoves trisaturates, optionally about 29° C.

In accordance with an embodiment of the invention a method produces atriglyceride oil characterized by a TAG profile. The method includesproviding an oleaginous plastidic host cell overexpressing a KASII gene,an exogenous FATA gene and an exogenous LPAAT gene, cultivating the cellso as to produce the oil, and isolating the oil; the TAG profile hasgreater than 50% SOS an less than 10% trisaturates.

In related embodiments, the cell includes a knockdown or knockout of anendogenous SAD2 gene and/or knockdown or knockout of an endogenous FATAgene. The exogenous FATA gene can encode a functional FATA acyl-ACPthioesterase protein with at least 90, 91, 92, 93, 94, 95, 96, 97, 98,or 99% sequence identity to SEQ ID NO: 92. The exogenous LPAAT gene canencode a functional Lysophosphatidic acid acyltransferase protein withat least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity toSEQ ID NO: 93. Optionally, the host cell can be a microalga, optionallyof Trebouxiophyceae, and optionally of the genus Chlorella orPrototheca, and optionally having 23S rRNA with at least 65, 70, 75, 80,85, 90 or 95% nucleotide sequence identity to SEQ ID NO: 76.

In an embodiment, a recombinant microlagal host cell optionally ofTrebouxiophyceae, and optionally of the genus Chlorella or Prototheca,and optionally having 23S rRNA with at least 65, 70, 75, 80, 85, 90 or95% nucleotide sequence identity to SEQ ID NO: 76, expresses anexogenous FATA gene encodes a functional FATA acyl-ACP thioesteraseprotein with at least 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99%sequence identity to SEQ ID NO: 92.

In an embodiment, a recombinant microlagal host cell optionally ofTrebouxiophyceae, and optionally of the genus Chlorella or Prototheca,and optionally having 23S rRNA with at least 65, 70, 75, 80, 85, 90 or95% nucleotide sequence identity to SEQ ID NO: 76, expresses anexogenous LPAAT gene encodes a functional Lysophosphatidic acidacyltransferase protein with at least 90, 91, 92, 93, 94, 95, 96, 97,98, or 99% sequence identity to SEQ ID NO: 93.

These and other aspects and embodiments of the invention are describedand/or exemplified in the accompanying drawings, a brief description ofwhich immediately follows, the detailed description of the invention,and in the examples. Any or all of the features discussed above andthroughout the application can be combined in various embodiments of thepresent invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1-14 show fatty acid profiles and melting curves of refined,bleached and deodorized oils from genetically engineered Protothecamoriformis strains, as discussed in Example 4;

FIG. 15 shows the stability of different oils as a function ofantioxidant concentration, as discussed in Example 5;

FIG. 16 shows various properties of cell oils with very low levels ofpolyunsaturated fatty acids in accordance with an embodiment of theinvention; and

FIG. 17 shows a plot of percent solid fat content for various oils asfollows: (a) P. moriformis RBD oil without lipid pathway engineering;(b) Brazilian cocoa butter+25% milk fat; (c) three replicates of P.moriformis RBD oil from a strain expressing hairpin nucleic acids thatreduce levels of a SAD allele thus reducing oleic acid and increasingstearic acid in the TAG profile; (d) P. moriformis RBD oil from a strainoverexpressing an endogenous OTE (oleoyl acyl-ACP thioesterase, seeExample 45); (e) Malaysian cocoa butter+25% milk fat; and (f) Malaysiancocoa butter. The cocoa butter and cocoa butter milk fat values areliterature values (Bailey's Industrial Oils and Fat Products, 6^(th)ed.).

FIG. 18 shows the results of thermal stability testing performed onmethylated oil prepared from high-oleic (HO) and high-stabilityhigh-oleic (HSAO) triglyceride oils prepared from heterotrophicallygrown oleaginous microalgae, in comparison to a soya methyl estercontrol sample.

FIG. 19 shows various properties of high-oleic and high-stabilityhigh-oleic algal oils.

FIG. 20 shows TAG composition of Strain K-4, Strain AU and Strain AVoils from flask and fermenter biomass. La=laurate (C12:0), M=myristate(C14:0), P=palmitate (C16:0), Po=palmitoleate (C16:1), S=stearate(C18:0), O=oleate (C18:1), L=linoleate (C18:2), Ln=α-linolenate (C18:3),A=arachidate (C20:0), B=behenate (C22:0), Lg=lignocerate (C24:0),Hx=hexacosanoate (C26:0) S-S-S refers to the sum of TAGs in which allthree fatty acids are saturated. In each block of bars, the strains areshown in the order illustrated at the bottom of the figure.

FIG. 21 shows TAG composition of Strain AW Strain AX and Strain AY oilsfrom shake flask biomass. La=laurate (C12:0), M=myristate (C14:0),P=palmitate (C16:0), Po=palmitoleate (C16:1), S=stearate (C18:0),O=oleate (C18:1), L=linoleate (C18:2), Ln=α-linolenate (C18:3),A=arachidate (C20:0), B=behenate (C22:0), Lg=lignocerate (C24:0),Hx=hexacosanoate (C26:0). S-S-S refers to the sum of TAGs in which allthree fatty acids are saturated. In each block of bars, the strains areshown in the order illustrated at the bottom of the figure.

FIG. 22 shows the fatty acid profile and solid fat content of a refined,bleached and deodorized myristate rich oil from a genetically engineeredPrototheca moriformis strain as discussed in Example 52.

FIG. 23 shows the pairwise alignment of heterologous FAE proteins (SEQID NOS 165-171, respectively, in order of appearance) expressed inSTRAIN Z.

FIG. 24 shows genetic modification of a microalgal strain to produceddouble knockouts of FAD2/FADc and FATA.

DETAILED DESCRIPTION OF THE INVENTION I. DEFINITIONS

An “allele” refers to a copy of a gene where an organism has multiplesimilar or identical gene copies, even if on the same chromosome. Anallele may encode the same or similar protein.

In connection with two fatty acids in a fatty acid profile, “balanced”shall mean that the two fatty acids are within a specified percentage oftheir mean area percent. Thus, for fatty acid a in x % abundance andfatty acid b in y % abundance, the fatty acids are “balanced to within z%” if |x−((x+y)/2)| and |y−((x+y)/2)| are ≤100(z).

A “cell oil” or “cell fat” shall mean a predominantly triglyceride oilobtained from an organism, where the oil has not undergone blending withanother natural or synthetic oil, or fractionation so as tosubstantially alter the fatty acid profile of the triglyceride. Inconnection with an oil comprising triglycerides of a particularregiospecificity, the cell oil or cell fat has not been subjected tointeresterification or other synthetic process to obtain thatregiospecific triglyceride profile, rather the regiospecificity isproduced naturally, by a cell or population of cells. For a cell oilproduced by a cell, the sterol profile of oil is generally determined bythe sterols produced by the cell, not by artificial reconstitution ofthe oil by adding sterols in order to mimic the cell oil. In connectionwith a cell oil or cell fat, and as used generally throughout thepresent disclosure, the terms oil and fat are used interchangeably,except where otherwise noted. Thus, an “oil” or a “fat” can be liquid,solid, or partially solid at room temperature, depending on the makeupof the substance and other conditions. Here, the term “fractionation”means removing material from the oil in a way that changes its fattyacid profile relative to the profile produced by the organism, howeveraccomplished. The terms “cell oil” and “cell fat” encompass such oilsobtained from an organism, where the oil has undergone minimalprocessing, including refining, bleaching and/or degumming, which doesnot substantially change its triglyceride profile. A cell oil can alsobe a “noninteresterified cell oil”, which means that the cell oil hasnot undergone a process in which fatty acids have been redistributed intheir acyl linkages to glycerol and remain essentially in the sameconfiguration as when recovered from the organism.

“Exogenous gene” shall mean a nucleic acid that codes for the expressionof an RNA and/or protein that has been introduced into a cell (e.g. bytransformation/transfection), and is also referred to as a “transgene”.A cell comprising an exogenous gene may be referred to as a recombinantcell, into which additional exogenous gene(s) may be introduced. Theexogenous gene may be from a different species (and so heterologous), orfrom the same species (and so homologous), relative to the cell beingtransformed. Thus, an exogenous gene can include a homologous gene thatoccupies a different location in the genome of the cell or is underdifferent control, relative to the endogenous copy of the gene. Anexogenous gene may be present in more than one copy in the cell. Anexogenous gene may be maintained in a cell as an insertion into thegenome (nuclear or plastid) or as an episomal molecule.

“FADc”, also referred to as “FAD2” is a gene encoding a delta-12 fattyacid desaturase.

“Fatty acids” shall mean free fatty acids, fatty acid salts, or fattyacyl moieties in a glycerolipid. It will be understood that fatty acylgroups of glycerolipids can be described in terms of the carboxylic acidor anion of a carboxylic acid that is produced when the triglyceride ishydrolyzed or saponified.

“Fixed carbon source” is a molecule(s) containing carbon, typically anorganic molecule that is present at ambient temperature and pressure insolid or liquid form in a culture media that can be utilized by amicroorganism cultured therein. Accordingly, carbon dioxide is not afixed carbon source.

“In operable linkage” is a functional linkage between two nucleic acidsequences, such a control sequence (typically a promoter) and the linkedsequence (typically a sequence that encodes a protein, also called acoding sequence). A promoter is in operable linkage with an exogenousgene if it can mediate transcription of the gene.

“Microalgae” are eukaryotic microbial organisms that contain achloroplast or other plastid, and optionally that is capable ofperforming photosynthesis, or a prokaryotic microbial organism capableof performing photosynthesis. Microalgae include obligatephotoautotrophs, which cannot metabolize a fixed carbon source asenergy, as well as heterotrophs, which can live solely off of a fixedcarbon source. Microalgae include unicellular organisms that separatefrom sister cells shortly after cell division, such as Chlamydomonas, aswell as microbes such as, for example, Volvox, which is a simplemulticellular photosynthetic microbe of two distinct cell types.Microalgae include cells such as Chlorella, Dunaliella, and Prototheca.Microalgae also include other microbial photosynthetic organisms thatexhibit cell-cell adhesion, such as Agmenellum, Anabaena, andPyrobotrys. Microalgae also include obligate heterotrophicmicroorganisms that have lost the ability to perform photosynthesis,such as certain dinoflagellate algae species and species of the genusPrototheca.

In connection with fatty acid length, “mid-chain” shall mean C8 to C16fatty acids.

In connection with a recombinant cell, the term “knockdown” refers to agene that has been partially suppressed (e.g., by about 1-95%) in termsof the production or activity of a protein encoded by the gene.

Also, in connection with a recombinant cell, the term “knockout” refersto a gene that has been completely or nearly completely (e.g., >95%)suppressed in terms of the production or activity of a protein encodedby the gene. Knockouts can be prepared by homologous recombination of anoncoding sequence into a coding sequence, gene deletion, mutation orother method.

An “oleaginous” cell is a cell capable of producing at least 20% lipidby dry cell weight, naturally or through recombinant or classical strainimprovement. An “oleaginous microbe” or “oleaginous microorganism” is amicrobe, including a microalga that is oleaginous (especially eukaryoticmicroalgae that store lipid). An oleaginous cell also encompasses a cellthat has had some or all of its lipid or other content removed, and bothlive and dead cells.

An “ordered oil” or “ordered fat” is one that forms crystals that areprimarily of a given polymorphic structure. For example, an ordered oilor ordered fat can have crystals that are greater than 50%, 60%, 70%,80%, or 90% of the β or β′ polymorphic form.

In connection with a cell oil, a “profile” is the distribution ofparticular species or triglycerides or fatty acyl groups within the oil.A “fatty acid profile” is the distribution of fatty acyl groups in thetriglycerides of the oil without reference to attachment to a glycerolbackbone. Fatty acid profiles are typically determined by conversion toa fatty acid methyl ester (FAME), followed by gas chromatography (GC)analysis with flame ionization detection (FID), as in Example 1. Thefatty acid profile can be expressed as one or more percent of a fattyacid in the total fatty acid signal determined from the area under thecurve for that fatty acid. FAME-GC-FID measurement approximate weightpercentages of the fatty acids. A “sn-2 profile” is the distribution offatty acids found at the sn-2 position of the triacylglycerides in theoil. A “regiospecific profile” is the distribution of triglycerides withreference to the positioning of acyl group attachment to the glycerolbackbone without reference to stereospecificity. In other words, aregiospecific profile describes acyl group attachment at sn-1/3 vs.sn-2. Thus, in a regiospecific profile, POS (palmitate-oleate-stearate)and SOP (stearate-oleate-palmitate) are treated identically. A“stereospecific profile” describes the attachment of acyl groups atsn-1, sn-2 and sn-3. Unless otherwise indicated, triglycerides such asSOP and POS are to be considered equivalent. A “TAG profile” is thedistribution of fatty acids found in the triglycerides with reference toconnection to the glycerol backbone, but without reference to theregiospecific nature of the connections. Thus, in a TAG profile, thepercent of SSO in the oil is the sum of SSO and SOS, while in aregiospecific profile, the percent of SSO is calculated withoutinclusion of SOS species in the oil. In contrast to the weightpercentages of the FAME-GC-FID analysis, triglyceride percentages aretypically given as mole percentages; that is the percent of a given TAGmolecule in a TAG mixture.

The term “percent sequence identity,” in the context of two or moreamino acid or nucleic acid sequences, refers to two or more sequences orsubsequences that are the same or have a specified percentage of aminoacid residues or nucleotides that are the same, when compared andaligned for maximum correspondence, as measured using a sequencecomparison algorithm or by visual inspection. For sequence comparison todetermine percent nucleotide or amino acid identity, typically onesequence acts as a reference sequence, to which test sequences arecompared. When using a sequence comparison algorithm, test and referencesequences are input into a computer, subsequence coordinates aredesignated, if necessary, and sequence algorithm program parameters aredesignated. The sequence comparison algorithm then calculates thepercent sequence identity for the test sequence(s) relative to thereference sequence, based on the designated program parameters. Optimalalignment of sequences for comparison can be conducted using the NCBIBLAST software (ncbi.nlm.nih.gov/BLAST/) set to default parameters. Forexample, to compare two nucleic acid sequences, one may use blastn withthe “BLAST 2 Sequences” tool Version 2.0.12 (Apr. 21, 2000) set at thefollowing default parameters: Matrix: BLOSUM62; Reward for match: 1;Penalty for mismatch: −2; Open Gap: 5 and Extension Gap: 2 penalties;Gap×drop-off: 50; Expect: 10; Word Size: 11; Filter: on. For a pairwisecomparison of two amino acid sequences, one may use the “BLAST 2Sequences” tool Version 2.0.12 (Apr. 21, 2000) with blastp set, forexample, at the following default parameters: Matrix: BLOSUM62; OpenGap: 11 and Extension Gap: 1 penalties; Gap×drop-off 50; Expect: 10;Word Size: 3; Filter: on.

“Recombinant” is a cell, nucleic acid, protein or vector that has beenmodified due to the introduction of an exogenous nucleic acid or thealteration of a native nucleic acid. Thus, e.g., recombinant cells canexpress genes that are not found within the native (non-recombinant)form of the cell or express native genes differently than those genesare expressed by a non-recombinant cell. Recombinant cells can, withoutlimitation, include recombinant nucleic acids that encode for a geneproduct or for suppression elements such as mutations, knockouts,antisense, interfering RNA (RNAi) or dsRNA that reduce the levels ofactive gene product in a cell. A “recombinant nucleic acid” is a nucleicacid originally formed in vitro, in general, by the manipulation ofnucleic acid, e.g., using polymerases, ligases, exonucleases, andendonucleases, using chemical synthesis, or otherwise is in a form notnormally found in nature. Recombinant nucleic acids may be produced, forexample, to place two or more nucleic acids in operable linkage. Thus,an isolated nucleic acid or an expression vector formed in vitro byligating DNA molecules that are not normally joined in nature, are bothconsidered recombinant for the purposes of this invention. Once arecombinant nucleic acid is made and introduced into a host cell ororganism, it may replicate using the in vivo cellular machinery of thehost cell; however, such nucleic acids, once produced recombinantly,although subsequently replicated intracellularly, are still consideredrecombinant for purposes of this invention. Similarly, a “recombinantprotein” is a protein made using recombinant techniques, i.e., throughthe expression of a recombinant nucleic acid.

The terms “triglyceride”, “triacylglyceride” and “TAG” are usedinterchangeably as is known in the art.

IL GENERAL

Illustrative embodiments of the present invention feature oleaginouscells that produce altered fatty acid profiles and/or alteredregiospecific distribution of fatty acids in glycerolipids, and productsproduced from the cells. Examples of oleaginous cells include microbialcells having a type II fatty acid biosynthetic pathway, includingplastidic oleaginous cells such as those of oleaginous algae and, whereapplicable, oil producing cells of higher plants including but notlimited to commercial oilseed crops such as soy, corn, rapeseed/canola,cotton, flax, sunflower, safflower and peanut. Other specific examplesof cells include heterotrophic or obligate heterotrophic microalgae ofthe phylum Chlorophtya, the class Trebouxiophytae, the orderChlorellales, or the family Chlorellacae. Examples of oleaginousmicroalgae and method of cultivation are also provided in Published PCTPatent Applications WO2008/151149, WO2010/06032, WO2011/150410, andWO2011/150411, including species of Chlorella and Prototheca, a genuscomprising obligate heterotrophs. The oleaginous cells can be, forexample, capable of producing 25, 30, 40, 50, 60, 70, 80, 85, or about90% oil by cell weight, ±5%. Optionally, the oils produced can be low inhighly unsaturated fatty acids such as DHA or EPA fatty acids. Forexample, the oils can comprise less than 5%, 2%, or 1% DHA and/or EPA.The above-mentioned publications also disclose methods for cultivatingsuch cells and extracting oil, especially from microalgal cells; suchmethods are applicable to the cells disclosed herein and incorporated byreference for these teachings. When microalgal cells are used they canbe cultivated autotrophically (unless an obligate heterotroph) or in thedark using a sugar (e.g., glucose, fructose and/or sucrose) In any ofthe embodiments described herein, the cells can be heterotrophic cellscomprising an exogenous invertase gene so as to allow the cells toproduce oil from a sucrose feedstock. Alternately, or in addition, thecells can metabolize xylose from cellulosic feedstocks. For example, thecells can be genetically engineered to express one or more xylosemetabolism genes such as those encoding an active xylose transporter, axylulose-5-phosphate transporter, a xylose isomerase, a xylulokinase, axylitol dehydrogenase and a xylose reductase. See WO2012/154626,“GENETICALLY ENGINEERED MICROORGANISMS THAT METABOLIZE XYLOSE”,published Nov. 15, 2012, including disclosure of genetically engineeredPrototheca strains that utilize xylose.

The oleaginous cells may, optionally, be cultivated in abioreactor/fermenter. For example, heterotrophic oleaginous microalgalcells can be cultivated on a sugar-containing nutrient broth.Optionally, cultivation can proceed in two stages: a seed stage and alipid-production stage. In the seed stage, the number of cells isincreased from s starter culture. Thus, the seeds stage typicallyincludes a nutrient rich, nitrogen replete, media designed to encouragerapid cell division. After the seeds stage, the cells may be fed sugarunder nutrient-limiting (e.g. nitrogen sparse) conditions so that thesugar will be converted into triglycerides. For example, the rate ofcell division in the lipid-production stage can be decreased by 50%, 80%or more relative to the seed stage. Additionally, variation in the mediabetween the seed stage and the lipid-production stage can induce therecombinant cell to express different lipid-synthesis genes and therebyalter the triglycerides being produced. For example, as discussed below,nitrogen and/or pH sensitive promoters can be placed in front ofendogenous or exogenous genes. This is especially useful when an oil isto be produced in the lipid-production phase that does not supportoptimal growth of the cells in the seed stage. In an example below, acell has a fatty acid desaturase with a pH sensitive promoter so than anoil that is low in linoleic acid is produced in the lipid productionstage while an oil that has adequate linoleic acid for cell division isproduced during the seed stage. The resulting low linoleic oil hasexceptional oxidative stability.

The oleaginous cells express one or more exogenous genes encoding fattyacid biosynthesis enzymes. As a result, some embodiments feature celloils that were not obtainable from a non-plant or non-seed oil, or notobtainable at all.

The oleaginous cells (optionally microalgal cells) can be improved viaclassical strain improvement techniques such as UV and/or chemicalmutagenesis followed by screening or selection under environmentalconditions, including selection on a chemical or biochemical toxin. Forexample the cells can be selected on a fatty acid synthesis inhibitor, asugar metabolism inhibitor, or an herbicide. As a result of theselection, strains can be obtained with increased yield on sugar,increased oil production (e.g., as a percent of cell volume, dry weight,or liter of cell culture), or improved fatty acid or TAG profile.

For example, the cells can be selected on one or more of1,2-Cyclohexanedione; 19-Norethindone acetate; 2,2-dichloropropionicacid; 2,4,5-trichlorophenoxyacetic acid; 2,4,5-trichlorophenoxyaceticacid, methyl ester; 2,4-dichlorophenoxyacetic acid;2,4-dichlorophenoxyacetic acid, butyl ester; 2,4-dichlorophenoxyaceticacid, isooctyl ester; 2,4-dichlorophenoxyacetic acid, methyl ester;2,4-dichlorophenoxybutyric acid; 2,4-dichlorophenoxybutyric acid, methylester; 2,6-dichlorobenzonitrile; 2-deoxyglucose;5-Tetradecyloxy-w-furoic acid; A-922500; acetochlor; alachlor; ametryn;amphotericin; atrazine; benfluralin; bensulide; bentazon; bromacil;bromoxynil; Cafenstrole; carbonyl cyanide m-chlorophenyl hydrazone(CCCP); carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP);cerulenin; chlorpropham; chlorsulfuron; clofibric acid; clopyralid;colchicine; cycloate; cyclohexamide; C75; DACTHAL (dimethyltetrachloroterephthalate); dicamba; dichloroprop((R)-2-(2,4-dichlorophenoxy)propanoic acid); Diflufenican;dihyrojasmonic acid, methyl ester; diquat; diuron; dimethylsulfoxide;Epigallocatechin gallate (EGCG); endothall; ethalfluralin; ethanol;ethofumesate; Fenoxaprop-p-ethyl; Fluazifop-p-Butyl; fluometuron;fomasefen; foramsulfuron; gibberellic acid; glufosinate ammonium;glyphosate; haloxyfop; hexazinone; imazaquin; isoxaben; Lipase inhibitorTHL ((−)-Tetrahydrolipstatin); malonic acid; MCPA(2-methyl-4-chlorophenoxyacetic acid); MCPB(4-(4-chloro-o-tolyloxy)butyric acid); mesotrione; methyldihydrojasmonate; metolachlor; metribuzin; Mildronate; molinate;naptalam; norharman; orlistat; oxadiazon; oxyfluorfen; paraquat;pendimethalin; pentachlorophenol; PF-04620110; phenethyl alcohol;phenmedipham; picloram; Platencin; Platensimycin; prometon; prometryn;pronamide; propachlor; propanil; propazine; pyrazon; Quizalofop-p-ethyl;s-ethyl dipropylthiocarbamate (EPTC); s,s,s-tributylphosphorotrithioate;salicylhydroxamic acid; sesamol; siduron; sodium methane arsenate;simazine; T-863 (DGAT inhibitor); tebuthiuron; terbacil; thiobencarb;tralkoxydim; triallate; triclopyr; triclosan; trifluralin; and vulpinicacid.

The oleaginous cells produce a storage oil, which is primarilytriacylglyceride and may be stored in storage bodies of the cell. A rawoil may be obtained from the cells by disrupting the cells and isolatingthe oil. The raw oil may comprise sterols produced by the cells.WO2008/151149, WO2010/06032, WO2011/150410, and WO2011/1504 discloseheterotrophic cultivation and oil isolation techniques for oleaginousmicroalgae. For example, oil may be obtained by providing orcultivating, drying and pressing the cells. The oils produced may berefined, bleached and deodorized (RBD) as known in the art or asdescribed in WO2010/120939. The raw or RBD oils may be used in a varietyof food, chemical, and industrial products or processes. Even after suchprocessing, the oil may retain a sterol profile characteristic of thesource. Microalgal sterol profiles are disclosed below. See especiallySection XII of this patent application. After recovery of the oil, avaluable residual biomass remains. Uses for the residual biomass includethe production of paper, plastics, absorbents, adsorbents, drillingfluids, as animal feed, for human nutrition, or for fertilizer.

Where a fatty acid profile of a triglyceride (also referred to as a“triacylglyceride” or “TAG”) cell oil is given here, it will beunderstood that this refers to a nonfractionated sample of the storageoil extracted from the cell analyzed under conditions in whichphospholipids have been removed or with an analysis method that issubstantially insensitive to the fatty acids of the phospholipids (e.g.using chromatography and mass spectrometry). The oil may be subjected toan RBD process to remove phospholipids, free fatty acids and odors yethave only minor or negligible changes to the fatty acid profile of thetriglycerides in the oil. Because the cells are oleaginous, in somecases the storage oil will constitute the bulk of all the TAGs in thecell. Examples 1, 2, and 8 below give analytical methods for determiningTAG fatty acid composition and regiospecific structure.

Broadly categorized, certain embodiments of the invention include (i)auxotrophs of particular fatty acids; (ii) cells that produce oilshaving low concentrations of polyunsaturated fatty acids, includingcells that are auxotrophic for unsaturated fatty acids; (iii) cellsproducing oils having high concentrations of particular fatty acids dueto expression of one or more exogenous genes encoding enzymes thattransfer fatty acids to glycerol or a glycerol ester; (iv) cellsproducing regiospecific oils, (v) genetic constructs or cells encoding anewly discovered gene encoding an LPAAT enzyme from Cuphea PSR23 (seeExample 43), (vi) cells producing low levels of saturated fatty acidsand/or high levels of palmitoleic acid, (vii) cells producing erucicacid, and (viii) other inventions related to producing cell oils withaltered profiles. The embodiments also encompass the oils made by suchcells, the residual biomass from such cells after oil extraction,oleochemicals, fuels and food products made from the oils and methods ofcultivating the cells.

In any of the embodiments below, the cells used are optionally cellshaving a type II fatty acid biosynthetic pathway such as microalgalcells including heterotrophic or obligate heterotrophic microalgalcells, including cells classified as Chlorophyta, Trebouxiophyceae ,Chlorellales, Chlorellaceae, or Chlorophyceae, or cells engineered tohave a type II fatty acid biosynthetic pathway using the tools ofsynthetic biology (i.e., transplanting the genetic machinery for a typeII fatty acid biosynthesis into an organism lacking such a pathway). Useof a host cell with a type II pathway avoids the potential fornon-interaction between an exogenous acyl-ACP thioesterase or otherACP-binding enzyme and the multienzyme complex of type I cellularmachinery. In specific embodiments, the cell is of the speciesPrototheca moriformis, Prototheca krugani, Prototheca stagnora orPrototheca zopfii or has a 23S rRNA sequence with at least 65, 70, 75,80, 85, 90 or 95% nucleotide identity SEQ ID NO: 76. By cultivating inthe dark or using an obligate heterotroph, the cell oil produced can below in chlorophyll or other colorants. For example, the cell oil canhave less than 100, 50, 10, 5, 1, 0.0.5 ppm of chlorophyll withoutsubstantial purification.

The stable carbon isotope value 613C is an expression of the ratio of¹³C/¹²C relative to a standard (e.g. PDB, carbonite of fossil skeletonof Belemnite americana from Peedee formation of South Carolina). Thestable carbon isotope value δ13C (‰) of the oils can be related to the613C value of the feedstock used. In some embodiments the oils arederived from oleaginous organisms heterotrophically grown on sugarderived from a C4 plant such as corn or sugarcane. In some embodimentsthe 613C (‰) of the oil is from −10 to −17‰ or from −13 to −16‰.

In specific embodiments and examples discussed below, one or more fattyacid synthesis genes (e.g., encoding an acyl-ACP thioesterase, aketo-acyl ACP synthase, an LPAAT, a stearoyl ACP desaturase, or othersdescribed herein) is incorporated into a microalga. It has been foundthat for certain microalga, a plant fatty acid synthesis gene product isfunctional in the absence of the corresponding plant acyl carrierprotein (ACP), even when the gene product is an enzyme, such as anacyl-ACP thioesterase, that requires binding of ACP to function. Thus,optionally, the microalgal cells can utilize such genes to make adesired oil without co-expression of the plant ACP gene.

For the various embodiments of recombinant cells comprising exogenousgenes or combinations of genes, it is contemplated that substitution ofthose genes with genes having 60, 70, 80, 85, 90, 91, 92, 93, 94, 95,96, 97, 98, or 99% nucleic acid sequence identity can give similarresults, as can substitution of genes encoding proteins having 60, 70,80, 85, 90, 91, 92, 93, 94, 95, 95.5, 96, 96.5, 97, 97.5, 98, 98.5, 99or 99.5% amino acid sequence identity. Likewise, for novel regulatoryelements, it is contemplated that substitution of those nucleic acidswith nucleic acids having 60, 70, 80, 85, 90, 91, 92, 93, 94, 95, 96,97, 98, or 99% nucleic acid can be efficacious. In the variousembodiments, it will be understood that sequences that are not necessaryfor function (e.g. FLAG® tags or inserted restriction sites) can oftenbe omitted in use or ignored in comparing genes, proteins and variants.

Although discovered using or exemplified with microalgae, the novelgenes and gene combinations reported here can be used in higher plantsusing techniques that are well known in the art. For example, the use ofexogenous lipid metabolism genes in higher plants is described in U.S.Pat. Nos. 6,028,247, 5,850,022, 5,639,790, 5,455,167, 5,512,482,and5,298,421 disclose higher plants with exogenous acyl-ACP thioesterases.WO2009129582 and WO1995027791 disclose cloning of LPAAT in plants. FAD2suppression in higher plants is taught in WO 2013112578, and WO2008006171.

As described in Example 63, transcript profiling was used to discoverpromoters that modulate expression in response to low nitrogenconditions. The promoters are useful to selectively express variousgenes and to alter the fatty acid composition of microbial oils. Inaccordance with an embodiment, there are non-natural constructscomprising a heterologous promoter and a gene, wherein the promotercomprises at least 60, 65, 70, 75, 80, 85, 90, or 95% sequence identityto any of the promoters of Example 63 (e.g., SEQ ID NOs: 130-147) andthe gene is differentially expressed under low vs. high nitrogenconditions. Optionally, the expression is less pH sensitive than for theAMT03 promoter. For example, the promoters can be placed in front of aFAD2 gene in a linoleic acid auxotroph to produce an oil with less than5, 4, 3, 2, or 1% linoleic acid after culturing under high, then lownitrogen conditions.

III. FATTY ACID AUXOTROPHS/REDUCING FATTY ACID LEVELS TO GROWTHINHIBITORY CONDITIONS DURING AN OIL PRODUCTION PHASE

In an embodiment, the cell is genetically engineered so that all allelesof a lipid pathway gene are knocked out. Alternately, the amount oractivity of the gene products of the alleles is knocked down so as torequire supplementation with fatty acids. A first transformationconstruct can be generated bearing donor sequences homologous to one ormore of the alleles of the gene. This first transformation construct maybe introduced and selection methods followed to obtain an isolatedstrain characterized by one or more allelic disruptions. Alternatively,a first strain may be created that is engineered to express a selectablemarker from an insertion into a first allele, thereby inactivating thefirst allele. This strain may be used as the host for still furthergenetic engineering to knockout or knockdown the remaining allele(s) ofthe lipid pathway gene (e.g., using a second selectable marker todisrupt a second allele). Complementation of the endogenous gene can beachieved through engineered expression of an additional transformationconstruct bearing the endogenous gene whose activity was originallyablated, or through the expression of a suitable heterologous gene. Theexpression of the complementing gene can either be regulatedconstitutively or through regulatable control, thereby allowing fortuning of expression to the desired level so as to permit growth orcreate an auxotrophic condition at will. In an embodiment, a populationof the fatty acid auxotroph cells are used to screen or select forcomplementing genes; e.g., by transformation with particular genecandidates for exogenous fatty acid synthesis enzymes, or a nucleic acidlibrary believed to contain such candidates.

Knockout of all alleles of the desired gene and complementation of theknocked-out gene need not be carried out sequentially. The disruption ofan endogenous gene of interest and its complementation either byconstitutive or inducible expression of a suitable complementing genecan be carried out in several ways. In one method, this can be achievedby co-transformation of suitable constructs, one disrupting the gene ofinterest and the second providing complementation at a suitable,alternative locus. In another method, ablation of the target gene can beeffected through the direct replacement of the target gene by a suitablegene under control of an inducible promoter (“promoter hijacking”). Inthis way, expression of the targeted gene is now put under the controlof a regulatable promoter. An additional approach is to replace theendogenous regulatory elements of a gene with an exogenous, induciblegene expression system. Under such a regime, the gene of interest cannow be turned on or off depending upon the particular needs. A stillfurther method is to create a first strain to express an exogenous genecapable of complementing the gene of interest, then to knockout out orknockdown all alleles of the gene of interest in this first strain. Theapproach of multiple allelic knockdown or knockout and complementationwith exogenous genes may be used to alter the fatty acid profile,regiospecific profile, sn-2 profile, or the TAG profile of theengineered cell.

Where a regulatable promoter is used, the promoter can be pH-sensitive(e.g., amt03), nitrogen and pH sensitive (e.g., amt03), or nitrogensensitive but pH-insensitive (e.g., newly discovered promoters ofExample 63) or variants thereof comprising at least 60, 65, 70, 75, 80,85, 90, 95, 96, 97, 98 or 99% sequence identity to any of theaforementioned promoters. In connection with a promoter, pH-insensitivemeans that the promoter is less sensitive than the amt03 promoter whenenvironmental conditions are shifter from pH 6.8 to 5.0 (e.g., at least5, 10, 15, or 20% less relative change in activity upon the pH-shift ascompared to an equivalent cell with amt03 as the promoter).

In a specific embodiment, the recombinant cell comprises nucleic acidsoperable to reduce the activity of an endogenous acyl-ACP thioesterase;for example a FatA or FatB acyl-ACP thioesterase having a preference forhydrolyzing fatty acyl-ACP chains of length C18 (e.g., stearate (C18:0)or oleate (C18:1), or C8:0-C16:0 fatty acids. The activity of anendogenous acyl-ACP thioesterase may be reduced by knockout or knockdownapproaches. Knockdown may be achieved, for example, through the use ofone or more RNA hairpin constructs, by promoter hijacking (substitutionof a lower activity or inducible promoter for the native promoter of anendogenous gene), or by a gene knockout combined with introduction of asimilar or identical gene under the control of an inducible promoter.Example 34 describes the engineering of a Prototheca strain in which twoalleles of the endogenous fatty acyl-ACP thioesterase (FATA1) have beenknocked out. The activity of the Prototheca moriformis FATA1 wascomplemented by the expression of an exogenous FatA or FatB acyl-ACPthioesterase. Example 36 details the use of RNA hairpin constructs toreduce the expression of FATA in Prototheca, which resulted in analtered fatty acid profile having less palmitic acid and more oleicacid.

Accordingly, oleaginous cells, including those of organisms with a typeII fatty acid biosynthetic pathway can have knockouts or knockdowns ofacyl-ACP thioesterase-encoding alleles to such a degree as to eliminateor severely limit viability of the cells in the absence of fatty acidsupplementation or genetic complementations. These strains can be usedto select for transformants expressing acyl-ACP-thioesterase transgenes.Alternately, or in addition, the strains can be used to completelytransplant exogenous acyl-ACP-thioesterases to give dramaticallydifferent fatty acid profiles of cell oils produced by such cells. Forexample, FATA expression can be completely or nearly completelyeliminated and replaced with FATB genes that produce mid-chain fattyacids. Alternately, an organism with an endogenous FatA gene havingspecificity for palmitic acid (C16) relative to stearic or oleic acid(C18) can be replaced with an exogenous FatA gene having a greaterrelative specificity for stearic acid (C18:0) or replaced with anexogenous FatA gene having a greater relative specificity for oleic acid(C18:1). In certain specific embodiments, these transformants withdouble knockouts of an endogenous acyl-ACP thioesterase produce celloils with more than 50, 60, 70, 80, or 90% caprylic, capric, lauric,myristic, or palmitic acid, or total fatty acids of chain length lessthan 18 carbons. Such cells may require supplementation with longerchain fatty acids such as stearic or oleic acid or switching ofenvironmental conditions between growth permissive and restrictivestates in the case of an inducible promoter regulating a FatA gene.

In an embodiment the oleaginous cells are cultured (e.g., in abioreactor). The cells are fully auxotrophic or partially auxotrophic(i.e., lethality or synthetic sickness) with respect to one or moretypes of fatty acid. The cells are cultured with supplementation of thefatty acid(s) so as to increase the cell number, then allowing the cellsto accumulate oil (e.g. to at least 40% by dry cell weight).Alternatively, the cells comprise a regulatable fatty acid synthesisgene that can be switched in activity based on environmental conditionsand the environmental conditions during a first, cell division, phasefavor production of the fatty acid and the environmental conditionsduring a second, oil accumulation, phase disfavor production of thefatty acid. In the case of an inducible gene, the regulation of theinducible gene can be mediated, without limitation, via environmental pH(for example, by using the AMT3 promoter as described in the Examples).

As a result of applying either of these supplementation or regulationmethods, a cell oil may be obtained from the cell that has low amountsof one or more fatty acids essential for optimal cell propagation.Specific examples of oils that can be obtained include those low instearic, linoleic and/or linolenic acids.

These cells and methods are illustrated in connection with lowpolyunsaturated oils in the section immediately below and in Example 6(fatty acid desaturase auxotroph) in connection with oils low inpolyunsaturated fatty acids and in Example 34 (acyl-ACP thioesteraseauxotroph).

Likewise, fatty acid auxotrophs can be made in other fatty acidsynthesis genes including those encoding a SAD, FAD, KASIII, KASI,KASII, KCS, elongase, GPAT, LPAAT, DGAT or AGPAT or PAP. Theseauxotrophs can also be used to select for complement genes or toeliminate native expression of these genes in favor of desired exogenousgenes in order to alter the fatty acid profile, regiospecific profile,or TAG profile of cell oils produced by oleaginous cells.

Accordingly, in an embodiment of the invention, there is a method forproducing an oil/fat. The method comprises cultivating a recombinantoleaginous cell in a growth phase under a first set of conditions thatis permissive to cell division so as to increase the number of cells dueto the presence of a fatty acid, cultivating the cell in an oilproduction phase under a second set of conditions that is restrictive tocell division but permissive to production of an oil that is depleted inthe fatty acid, and extracting the oil from the cell, wherein the cellhas a mutation or exogenous nucleic acids operable to suppress theactivity of a fatty acid synthesis enzyme, the enzyme optionally being astearoyl-ACP desaturase, delta 12 fatty acid desaturase, or aketoacyl-ACP synthase. The oil produced by the cell can be depleted inthe fatty acid by at least 50, 60, 70, 80, or 90%. The cell can becultivated heterotrophically. The cell can be a microalgal cellcultivated heterotrophically or autotrophically and may produce at least40, 50, 60, 70, 80, or 90% oil by dry cell weight.

IV. (A) LOW POLYUNSATURATED CELL OILS

In an embodiment of the present invention, the cell oil produced by thecell has very low levels of polyunsaturated fatty acids. As a result,the cell oil can have improved stability, including oxidative stability.The cell oil can be a liquid or solid at room temperature, or a blend ofliquid and solid oils, including the regiospecific or stereospecificoils, high stearate oils, or high mid-chain oils described infra.Oxidative stability can be measured by the Rancimat method using the AOCS Cd 12b-92 standard test at a defined temperature. For example, the OSI(oxidative stability index) test may be run at temperatures between 110°C. and 140° C. The oil is produced by cultivating cells (e.g., any ofthe plastidic microbial cells mentioned above or elsewhere herein) thatare genetically engineered to reduce the activity of one or more fattyacid desaturase. For example, the cells may be genetically engineered toreduce the activity of one or more fatty acyl Δ12 desaturase(s)responsible for converting oleic acid (18:1) into linoleic acid (18:2)and/or one or more fatty acyl 415 desaturase(s) responsible forconverting linoleic acid (18:2) into linolenic acid (18:3). Variousmethods may be used to inhibit the desaturase including knockout ormutation of one or more alleles of the gene encoding the desaturase inthe coding or regulatory regions, inhibition of RNA transcription, ortranslation of the enzyme, including RNAi, siRNA, miRNA, dsRNA,antisense, and hairpin RNA techniques. Other techniques known in the artcan also be used including introducing an exogenous gene that producesan inhibitory protein or other substance that is specific for thedesaturase. In specific examples, a knockout of one fatty acyl Δ12desaturase allele is combined with RNA-level inhibition of a secondallele.

In a specific embodiment, fatty acid desaturase (e.g., Δ12 fatty aciddesaturase) activity in the cell is reduced to such a degree that thecell is unable to be cultivated or is difficult to cultivate (e.g., thecell division rate is decreased more than 10, 20, 30, 40, 50, 60, 70,80, 90, 95, 97 or 99%). Achieving such conditions may involve knockout,or effective suppression of the activity of multiple gene copies (e.g.2, 3, 4 or more) of the desaturase or their gene products. A specificembodiment includes the cultivation in cell culture of a full or partialfatty acid auxotroph with supplementation of the fatty acid or a mixtureof fatty acids so as to increase the cell number, then allowing thecells to accumulate oil (e.g. to at least 40% by cell weight).Alternatively, the cells comprise a regulatable fatty acid synthesisgene that can be switched in activity. For example, the regulation canbe based on environmental conditions and the environmental conditionsduring a first, cell division, phase favor production of the fatty acidand the environmental conditions during a second, oil accumulation,phase disfavor production of the oil. For example, culture media pHand/or nitrogen levels can be used as an environmental control to switchexpression of a lipid pathway gene to produce a state of high or lowsynthetic enzyme activity. Examples of such cells are described inExample 7.

In a specific embodiment, a cell is cultivated using a modulation oflinoleic acid levels within the cell. In particular, the cell oil isproduced by cultivating the cells under a first condition that ispermissive to an increase in cell number due to the presence of linoleicacid and then cultivating the cells under a second condition that ischaracterized by linoleic acid starvation and thus is inhibitory to celldivision, yet permissive of oil accumulation. For example, a seedculture of the cells may be produced in the presence of linoleic acidadded to the culture medium. For example, the addition of linoleic acidto 0.25 g/L in the seed culture of a Prototheca strain deficient inlinoleic acid production due to ablation of two alleles of a fatty acylΔ12 desaturase (i.e., a linoleic auxotroph) was sufficient to supportcell division to a level comparable to that of wild type cells.Optionally, the linoleic acid can then be consumed by the cells, orotherwise removed or diluted. The cells are then switched into an oilproducing phase (e.g., supplying sugar under nitrogen limitingconditions such as described in WO2010/063032). Surprisingly, oilproduction has been found to occur even in the absence of linoleic acidproduction or supplementation, as demonstrated in the obligateheterotroph oleaginous microalgae Prototheca but generally applicable toother oleaginous microalgae, microorganisms, or even multicellularorganisms (e.g., cultured plant cells). Under these conditions, the oilcontent of the cell can increase to about 10, 20, 30, 40, 50, 60, 70,80, 90%, or more by dry cell weight, while the oil produced can havepolyunsaturated fatty acid (e.g.; linoleic+linolenic) profile with 5%,4%, 3%, 2%, 1%, 0.5%, 0.3%, 0.2%, 0.1%, 0.05% or less, as a percent oftotal triacylglycerol fatty acids in the oil. For example, the oilcontent of the cell can be 50% or more by dry cell weight and thetriglyceride of the oil produced less than 3% polyunsaturated fattyacids.

These oils can also be produced without the need (or reduced need) tosupplement the culture with linoleic acid by using cell machinery toproduce the linoleic acid during the cell division phase, but less or nolinoleic acid in the lipid production phase. The linoleic-producing cellmachinery may be regulatable so as to produce substantially lesslinoleic acid during the oil producing phase. The regulation may be viamodulation of transcription of the desaturase gene(s) or modulation ormodulation of production of an inhibitor substance (e.g., regulatedproduction of hairpin RNA/RNAi). For example, the majority, andpreferably all, of the fatty acid Δ12 desaturase activity can be placedunder a regulatable promoter regulated to express the desaturase in thecell division phase, but to be reduced or turned off during the oilaccumulation phase. The regulation can be linked to a cell culturecondition such as pH, and/or nitrogen level, as described in theexamples herein, or other environmental condition. In practice, thecondition may be manipulated by adding or removing a substance (e.g.,protons via addition of acid or base) or by allowing the cells toconsume a substance (e.g., nitrogen-supplying nutrients) to effect thedesired switch in regulation of the desaturase activity.

Other genetic or non-genetic methods for regulating the desaturaseactivity can also be used. For example, an inhibitor of the desaturasecan be added to the culture medium in a manner that is effective toinhibit polyunsaturated fatty acids from being produced during the oilproduction phase.

Accordingly, in a specific embodiment of the invention, there is amethod comprising providing a recombinant cell having a regulatabledelta 12 fatty acid desaturase gene, under control of a recombinantregulatory element via an environmental condition. The cell iscultivated under conditions that favor cell multiplication. Uponreaching a given cell density, the cell media is altered to switch thecells to lipid production mode by nutrient limitation (e.g. reduction ofavailable nitrogen). During the lipid production phase, theenvironmental condition is such that the activity of the delta 12 fattyacid desaturase is downregulated. The cells are then harvested and,optionally, the oil extracted. Due to the low level of delta 12 fattyacid desaturase during the lipid production phase, the oil has lesspolyunsaturated fatty acids and has improved oxidative stability.Optionally the cells are cultivated heterotrophically and optionallymicroalgal cells.

Using one or more of these desaturase regulation methods, it is possibleto obtain a cell oil that it is believed has been previouslyunobtainable, especially in large scale cultivation in a bioreactor(e.g., more than 1000 L). The oil can have polyunsaturated fatty acidlevels that are 5%, 4%, 3%, 2%, 1%, 0.5%, 0.3%, 0.2%, or less, as anarea percent of total triacylglycerol fatty acids in the oil.

One consequence of having such low levels of polyunsaturates is thatoils are exceptionally stable to oxidation. Indeed, in some cases theoils may be more stable than any previously known cell cell oil. Inspecific embodiments, the oil is stable, without added antioxidants, at110° C. so that the inflection point in conductance is not yet reachedby 10 hours, 15 hours, 20 hours, 30 hours, 40, hours, 50 hours, 60hours, or 70 hours under conditions of the AOCS Cd 12b-92. Rancimattest, noting that for very stable oils, replenishment of water may berequired in such a test due to evaporation that occurs with such longtesting periods (see Example 5). For example the oil can have and OSIvalue of 40-50 hours or 41-46 hours at 110° C. without addedantioxidants. When antioxidants (suitable for foods or otherwise) areadded, the OSI value measured may be further increased. For example,with added tocopherol (100ppm) and ascorbyl palmitate (500 ppm) or PANAand ascorbyl palmitate, such an oil can have an oxidative stabilityindex (OSI value) at 110° C. in excess 100 or 200 hours, as measured bythe Rancimat test. In another example, 1050 ppm of mixed tocopherols and500 pm of ascorbyl palmitate are added to an oil comprising less than 1%linoleic acid or less than 1% linoleic+linolenic acids; as a result, theoil is stable at 110° C. for 1, 2, 3, 4, 5, 6, 7, 8, or 9, 10, 11, 12,13, 14, 15, or 16, 20, 30, 40 or 50 days, 5 to 15 days, 6 to 14 days, 7to 13 days, 8 to 12 days, 9 to 11 days, about 10 days, or about 20 days.The oil can also be stable at 130° C. for 1, 2, 3, 4, 5, 6, 7, 8, or 9,10, 11, 12, 13, 14, 15, or 16, 20, 30, 40 or 50 days, 5 to 15 days, 6 to14 days, 7 to 13 days, 8 to 12 days, 9 to 11 days, about 10 days, orabout 20 days. In a specific example, such an oil was found to be stablefor greater than 100 hours (about 128 hours as observed). In a furtherembodiment, the OSI value of the cell oil without added antioxidants at120° C. is greater than 15 hours or 20 hours or is in the range of10-15, 15-20, 20-25, or 25-50 hours, or 50-100 hours.

In an example, using these methods, the oil content of a microalgal cellis between 40 and about 85% by dry cell weight and the polyunsaturatedfatty acids in the fatty acid profile of the oil is between 0.001% and3% in the fatty acid profile of the oil and optionally yields a cell oilhaving an OSI induction time of at least 20 hours at 110° C. without theaddition of antioxidants. In yet another example, there is a cell oilproduced by RBD treatment of a cell oil from an oleaginous cell, the oilcomprises between 0.001% and 2% polyunsaturated fatty acids and has anOSI induction time exceeding 30 hours at 110C without the addition ofantioxidants. In yet another example, there is a cell oil produced byRBD treatment of a cell oil from an oleaginous cell, the oil comprisesbetween 0.001% and 1% polyunsaturated fatty acids and has an OSIinduction time exceeding 30 hours at 110C without the addition ofantioxidants.

In another specific embodiment there is an oil with reducedpolyunsaturate levels produced by the above-described methods. The oilis combined with antioxidants such as PANA and ascorbyl palmitate. Forexample, it was found that when such an oil was combined with 0.5% PANAand 500ppm of ascorbyl palmitate the oil had an OSI value of about 5days at 130° C. or 21 days at 110° C. These remarkable results suggestthat not only is the oil exceptionally stable, but these twoantioxidants are exceptionally potent stabilizers of triglyceride oilsand the combination of these antioxidants may have general applicabilityincluding in producing stable biodegradable lubricants (e.g., jet enginelubricants). In specific embodiments, the genetic manipulation of fattyacyl Δ12 desaturase results in a 2 to 30, or 5 to 25, or 10 to 20 foldincrease in OSI (e.g., at 110° C.) relative to a strain without themanipulation. The oil can be produced by suppressing desaturase activityin a cell, including as described above.

Antioxidants suitable for use with the oils of the present inventioninclude alpha, delta, and gamma tocopherol (vitamin E), tocotrienol,ascorbic acid (vitamin C), glutathione, lipoic acid, uric acid,(3-carotene, lycopene, lutein, retinol (vitamin A), ubiquinol (coenzymeQ), melatonin, resveratrol, flavonoids, rosemary extract, propyl gallate(PG), tertiary butylhydroquinone (TBHQ), butylated hydroxyanisole (BHA),and butylated hydroxytoluene (BHT),N,N′-di-2-butyl-1,4-phenylenediamine,2,6-di-tert-butyl-4-methylphenol,2,4-dimethyl-6-tert-butylphenol, 2,4-dimethyl-6-tert-butylphenol,2,4-dimethyl-6-tert-butylphenol, 2,6-di-tert-butyl-4-methylphenol,2,6-di-tert-butylphenol, and phenyl-alpha-naphthylamine (PANA).

In addition to the desaturase modifications, in a related embodimentother genetic modifications may be made to further tailor the propertiesof the oil, as described throughout, including introduction orsubstitution of acyl-ACP thioesterases having altered chain lengthspecificity and/or overexpression of an endogenous or exogenous geneencoding a KAS, SAD, LPAAT, or DGAT gene. For example, a strain thatproduces elevated oleic levels may also produce low levels ofpolyunsaturates. Such genetic modifications can include increasing theactivity of stearoyl-ACP desaturase (SAD) by introducing an exogenousSAD gene, increasing elongase activity by introducing an exogenous KASIIgene, and/or knocking down or knocking out a FATA gene.

In a specific embodiment, a high oleic cell oil with low polyunsaturatesmay be produced. For example, the oil may have a fatty acid profile withgreater than 60, 70, 80, 90, or 95% oleic acid and less than 5, 4, 3, 2,or 1% polyunsaturates. In related embodiments, a cell oil is produced bya cell having recombinant nucleic acids operable to decrease fatty acidΔ12 desaturase activity and optionally fatty acid 415 desaturase so asto produce an oil having less than or equal to 3% polyunsaturated fattyacids with greater than 60% oleic acid, less than 2% polyunsaturatedfatty acids and greater than 70% oleic acid, less than 1%polyunsaturated fatty acids and greater than 80% oleic acid, or lessthan 0.5% polyunsaturated fatty acids and greater than 90% oleic acid.It has been found that one way to increase oleic acid is to userecombinant nucleic acids operable to decrease expression of a FATAacyl-ACP thioesterase and optionally overexpress a KAS II gene; such acell can produce an oil with greater than or equal to 75% oleic acid.Alternately, overexpression of KASII can be used without the FATAknockout or knockdown. Oleic acid levels can be further increased byreduction of delta 12 fatty acid desaturase activity using the methodsabove, thereby decreasing the amount of oleic acid the is converted intothe unsaturates linoleic acid and linolenic acid. Thus, the oil producedcan have a fatty acid profile with at least 75% oleic and at most 3%,2%, 1%, or 0.5% linoleic acid. In a related example, the oil has between80 to 95% oleic acid and about 0.001 to 2% linoleic acid, 0.01 to 2%linoleic acid, or 0.1 to 2% linoleic acid. In another relatedembodiment, an oil is produced by cultivating an oleaginous cell (e.g.,a microalga) so that the microbe produces a cell oil with less than 10%palmitic acid, greater than 85% oleic acid, 1% or less polyunsaturatedfatty acids, and less than 7% saturated fatty acids. See Example 58 inwhich such an oil is produced in a microalga with FAD and FATA knockoutsplus expression of an exogenous KASII gene. Such oils will have a lowfreezing point, with excellent stability and are useful in foods, forfrying, fuels, or in chemical applications. Further, these oils mayexhibit a reduced propensity to change color over time. In anillustrative chemical application, the high oleic oil is used to producea chemical. The oleic acid double bonds of the oleic acid groups of thetriglycerides in the oil can be epoxidized or hydroxylated to make apolyol. The epoxidized or hydroxylated oil can be used in a variety ofapplications. One such application is the production of polyurethane(including polyurethane foam) via condensation of the hydroxylatedtriglyceride with an isocyanate, as has been practiced with hydroxylatedsoybean oil or castor oil. See, e.g. US2005/0239915, US2009/0176904,US2005/0176839, US2009/0270520, and U.S. Pat. No. 4,264,743 andZlatanic, et al, Biomacromolecules 2002, 3, 1048-1056 (2002) forexamples of hydroxylation and polyurethane condensation chemistries.Suitable hydroxyl forming reactions include epoxidation of one or moredouble bonds of a fatty acid followed by acid catalyzed epoxide ringopening with water (to form a diol), alcohol (to form a hydroxyl ether),or an acid (to form a hydroxyl ester). There are multiple advantages ofusing the high-oleic/low polyunsaturated oil in producing a bio-basedpolyurethane: (1) the shelf-life, color or odor, of polyurethane foamsmay be improved; (2) the reproducibility of the product may be improveddue to lack of unwanted side reactions resulting from polyunsaturates;(3) a greater degree of hydroxylation reaction may occur due to lack ofpolyunsaturates and the structural characteristics of the polyurethaneproduct can be improved accordingly.

The low-polyunsaturated or high-oleic/low-polyunsaturated oils describedhere may be advantageously used in chemical applications where yellowingis undesirable. For example, yellowing can be undesirable in paints orcoatings made from the triglycerides fatty acids derived from thetriglycerides. Yellowing may be caused by reactions involvingpolyunsaturated fatty acids and tocotrienols and/or tocopherols. Thus,producing the high-stability oil in an oleaginous microbe with lowlevels of tocotrienols can be advantageous in elevating high colorstability a chemical composition made using the oil. In contrast tocommonly used plant oils, through appropriate choice of oleaginousmicrobe, the cell oils of these embodiments can have tocopherols andtocotrienols levels of 1 g/L or less. In a specific embodiment, a celloil has a fatty acid profile with less than 2% with polyunsaturatedfatty acids and less than 1 g/L for tocopherols, tocotrienols or the sumof tocopherols and tocotrienols. In another specific embodiment, thecell oil has a fatty acid profile with less than 1% with polyunsaturatedfatty acids and less than 0.5 g/L for tocopherols, tocotrienols or thesum of tocopherols and tocotrienols

Any of the high-stability (low-polyunsaturate) cell oils or derivativesthereof can be used to formulate foods, drugs, vitamins, nutraceuticals,personal care or other products, and are especially useful foroxidatively sensitive products. For example, the high-stability cell oil(e.g., less than or equal to 3%, 2% or 1% polyunsaturates) can be usedto formulate a sunscreen (e.g. a composition having one or more ofavobenzone, homosalate, octisalate, octocrylene or oxybenzone) orretinoid face cream with an increased shelf life due to the absence offree-radical reactions associated with polyunsaturated fatty acids. Forexample, the shelf-life can be increased in terms of color, odor,organoleptic properties or %active compound remaining after accelerateddegradation for 4 weeks at 54° C. The high stability oil can also beused as a lubricant with excellent high-temperature stability. Inaddition to stability, the oils can be biodegradable, which is a rarecombination of properties.

In another related embodiment, the fatty acid profile of a cell oil iselevated in C8 to C16 fatty acids through additional geneticmodification, e.g. through overexpression of a short-chain to mid chainpreferring acyl-ACP thioesterase or other modifications described here.A low polyunsaturated oil in accordance with these embodiments can beused for various industrial, food, or consumer products, including thoserequiring improved oxidative stability. In food applications, the oilsmay be used for frying with extended life at high temperature, orextended shelf life.

Where the oil is used for frying, the high stability of the oil mayallow for frying without the addition of antioxidant and/or defoamers(e.g. silicone). As a result of omitting defoamers, fried foods mayabsorb less oil. Where used in fuel applications, either as atriglyceride or processed into biodiesel or renewable diesel (see, e.g.,WO2008/151149 WO2010/063032, and WO2011/150410), the high stability canpromote storage for long periods, or allow use at elevated temperatures.For example, the fuel made from the high stability oil can be stored foruse in a backup generator for more than a year or more than 5 years. Thefrying oil can have a smoke point of greater than 200° C., and freefatty acids of less than 0.1% (either as a cell oil or after refining).

The low polyunsaturated oils may be blended with food oils, includingstructuring fats such as those that form beta or beta prime crystals,including those produced as described below. These oils can also beblended with liquid oils. If mixed with an oil having linoleic acid,such as corn oil, the linoleic acid level of the blend may approximatethat of high oleic plant oils such as high oleic sunflower oils (e.g.,about 80% oleic and 8% linoleic).

Blends of the low polyunsaturated cell oil can be interesterified withother oils. For example, the oil can be chemically or enzymaticallyinteresterified. In a specific embodiment, a low polyunsaturated oilaccording to an embodiment of the invention has at least 10% oleic acidin its fatty acid profile and less than 5% polyunsaturates and isenzymatically interesterified with a high saturate oil (e.g.hydrogenated soybean oil or other oil with high stearate levels) usingan enzyme that is specific for sn-1 and sn-2 triacylglycerol positions.The result is an oil that includes a stearate-oleate-stearate (SOS).Methods for interesterification are known in the art; see for example,“Enzymes in Lipid Modification,” Uwe T. Bornschuer, ed., Wiley_VCH,2000, ISBN 3-527-30176-3.

High stability oils can be used as spray oils. For example, dried fruitssuch as raisins can be sprayed with a high stability oil having lessthan 5, 4, 3, 2, or 1% polyunsaturates. As a result, the spray nozzleused will become clogged less frequently due to polymerization oroxidation product buildup in the nozzle that might otherwise result fromthe presence of polyunsaturates.

In a further embodiment, an oil that is high is SOS, such as thosedescribed below can be improved in stability by knockdown or regulationof delta 12 fatty acid desaturase.

Optionally, where the FADc promoter is regulated, it can be regulatedwith a promoter that is operable at low pH (e.g., one for which thelevel of transcription of FADc is reduced by less than half uponswitching from cultivation at pH 7.0 to cultivation at pH 5.0). Thepromoter can be sensitive to cultivation under low nitrogen conditionssuch that the promoter is active under nitrogen replete conditions andinactive under nitrogen starved conditions. For example, the promotermay cause a reduction in FADc transcript levels of 5, 10, 15-fold ormore upon nitrogen starvation. Because the promoter is operable at pH5.0, more optimal invertase activity can be obtained. For example, thecell can be cultivated in the presence of invertase at a pH of less than6.5, 6.0 or 5.5. The cell may have a FADc knockout to increase therelative gene-dosage of the regulated FADc. Optionally, the invertase isproduced by the cell (natively or due to an exogenous invertase gene).Because the promoter is less active under nitrogen starved conditions,fatty acid production can proceed during the lipid production phase thatwould not allow for optimal cell proliferation in the cell proliferationstage. In particular, a low linoleic oil may be produced. The cell canbe cultivated to an oil content of at least 20% lipid by dry cellweight. The oil may have a fatty acid profile having less than 5, 4, 3,2, 1, or 0.5, 0.2, or 0.1% linoleic acid. Example 62 describes thediscovery of such promoters.

IV. (B) HIGH 18:2/LOW 18:3 OILS OBTAINED USING FAD GENE REPLACEMENT

Surprisingly, while researching the production of low polyunsaturateoils as described above, an oil with high polyunsaturates but having aunique fatty acid profile was discovered. The discovery of this oil isdescribed in Example 59. Thus, it is possible to use an oleaginousplastidic cell (e.g., microalgal) culture to produce an oil with a fattyacid profile characterized by 10% or less linolenic acid (C18:3) and 20%or more linoleic acid (C18:2). Such oils can be produced in anoleaginous microalga or other oleaginous plastidic cell byoverexpression of a (endogenous or exogenous) KASII and gene replacementof FADc (also referred to as FAD2) and, if necessary based on the hostcell, replacing native acyl-ACP thioesterase activity. In Example 58-59,an endogenous KASII was overexpressed and an endogenous FADc gene wasplaced under control of a pH-inducible promoter, although constitutiveexpression would also work. Interestingly, the oils were much higher inlinoleic acid when the FADc was overexpressed in a linoleic acidauxotroph (e.g., a FADc double knockout). It is believed that this isdue to the presence of a previously unrecognized gene-level regulatorysystem in microalgae that must be disabled in order to efficientlyaccumulate linoleic acid. In addition, two copies of the endogenousacyl-ACP thioesterase were knocked out and replaced with anoleate-specific plant acyl-ACP thioesterase. Under permissive pHconditions, an oil with 10% or less linolenic acid (C18:3) and 20% ormore linoleic acid (C18:2). The oil can be extracted and used forvarious uses included in foodstuffs or chemicals. If the host cell is amicroalga, the oil can comprise microalgal sterols. As with otherembodiments, the host cell can be a microalga transformed to express anexogenous invertase, thus enable conversion of sucrose into the oilunder conditions of heterotrophic cultivation.

In a specific embodiment, a host cell comprises a FADc knockdown,knockout, or FADc with a down-regulatable promoter combined with anexogenous KASII gene that expresses a protein having at least 80, 85,90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% amino acid identity to theprotein encoded by the Prototheca moriformis KASII gene disclose inExample 58, and optionally expresses an acyl-ACP thioesterase geneproducing an oleate-specific acyl-ACP thioesterase enzyme. Optionally,the cell can be an a plant cell, a microbial cell, or a microalgal cell.

V. CELLS WITH EXOGENOUS ACYLTRANSFERASES

In various embodiments of the present invention, one or more genesencoding an acyltransferase (an enzyme responsible for the condensationof a fatty acid with glycerol or a glycerol derivative to form anacylglyceride) can be introduced into an oleaginous cell (e.g., aplastidic microalgal cell) so as to alter the fatty acid composition ofa cell oil produced by the cell. The genes may encode one or more of aglycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acidacyltransferase (LPAAT), also known as 1-acylglycerol-3-phosphateacyltransferase (AGPAT), phosphatidic acid phosphatase (PAP), ordiacylglycerol acyltransferase (DGAT) that transfers an acyl group tothe sn-3 position of DAG, thereby producing a TAG.

Recombinant nucleic acids may be integrated into a plasmid or chromosomeof the cell. Alternately, the gene encodes an enzyme of a lipid pathwaythat generates TAG precursor molecules through fattyacyl-CoA-independent routes separate from that above. Acyl-ACPs may besubstrates for plastidial GPAT and LPAAT enzymes and/or mitochondrialGPAT and LPAAT enzymes. Among further enzymes capable of incorporatingacyl groups (e.g., from membrane phospholipids) to produce TAGs isphospholipid diacylglycerol acyltransferase (PDAT). Still furtheracyltransferases, including lysophosphosphatidylcholine acyltransferase(LPCAT), lysophosphosphatidylserine acyltransferase (LPSAT),lysophosphosphatidylethanolamine acyltransferase (LPEAT), andlysophosphosphatidylinositol acyltransferase (LPIAT), are involved inphospholipid synthesis and remodeling that may impact triglyceridecomposition.

The exogenous gene can encode an acyltransferase enzyme havingpreferential specificity for transferring an acyl substrate comprising aspecific number of carbon atoms and/or a specific degree of saturationis introduced into a oleaginous cell so as to produce an oil enriched ina given regiospecific triglyceride. For example, the coconut (Cocosnucifera) lysophosphatidic acid acyltransferase has been demonstrated toprefer C12:0-CoA substrates over other acyl-CoA substrates (Knutzon etal., Plant Physiology, Vol. 120, 1999, pp. 739-746), whereas the1-acyl-sn-3-glycerol-3-phosphate acyltransferase of maturing safflowerseeds shows preference for linoleoyl-CoA and oleoyl-CoA substrates overother acyl-CoA substrates, including stearoyl-CoA (Ichihara et al.,European Journal of Biochemistry, Vol. 167, 1989, pp. 339-347).Furthermore, acyltransferase proteins may demonstrate preferentialspecificity for one or more short-chain, medium-chain, or long-chainacyl-CoA or acyl-ACP substrates, but the preference may only beencountered where a particular, e.g. medium-chain, acyl group is presentin the sn-1 or sn-3 position of the lysophosphatidic acid donorsubstrate. As a result of the exogenous gene, a TAG oil can be producedby the cell in which a particular fatty acid is found at the sn-2position in greater than 20, 30, 40, 50, 60, 70, 90, or 90% of the TAGmolecules.

In some embodiments of the invention, the cell makes an oil rich insaturated-unsaturated-saturated (sat-unsat-sat) TAGs. Sat-unsat-sat TAGSinclude 1,3-dihexadecanoyl-2-(9Z-octadecenoyl)-glycerol (referred to as1-palmitoyl-2-oleyl-glycero-3-palmitoyl),1,3-dioctadecanoyl-2-(9Z-octadecenoyl)-glycerol (referred to as1-stearoyl-2-oleyl-glycero-3-stearoyl), and1-hexadecanoyl-2-(9Z-octadecenoyl)-3-octadecanoy-glycerol (referred toas 1-palmitoyl-2-oleyl-glycero-3-stearoyl). These molecules are morecommonly referred to as POP, SOS, and POS, respectively, where ‘P’represents palmitic acid, ‘S’ represents stearic acid, and ‘O’represents oleic acid. Further examples ofsaturated-unsaturated-saturated TAGs include MOM, LOL, MOL, COC and COL,where ‘M’ represents myristic acid, ‘L’ represents lauric acid, and ‘C’represents capric acid (C8:0). Trisaturates, triglycerides with threesaturated fatty acyl groups, are commonly sought for use in foodapplications for their greater rate of crystallization than other typesof triglycerides. Examples of trisaturates include PPM, PPP, LLL, SSS,CCC, PPS, PPL, PPM, LLP, and LLS. In addition, the regiospecificdistribution of fatty acids in a TAG is an important determinant of themetabolic fate of dietary fat during digestion and absorption.

According to certain embodiments of the present invention, oleaginouscells are transformed with recombinant nucleic acids so as to producecell oils that comprise an elevated amount of a specified regiospecifictriglyceride, for example 1-acyl-2-oleyl-glycero-3-acyl, or1-acyl-2-lauric-glycero-3-acyl where oleic or lauric acid respectivelyis at the sn-2 position, as a result of introduced recombinant nucleicacids. Alternately, caprylic, capric, myristic, or palmitic acid may beat the sn-2 position. The amount of the specified regiospecifictriglyceride present in the cell oil may be increased by greater than5%, greater than 10%, greater than 15%, greater than 20%, greater than25%, greater than 30%, greater than 35%, greater than 40%, greater than50%, greater than 60%, greater than 70%, greater than 80%, greater than90%, greater than 100-500%, or greater than 500% than in the cell oilproduced by the microorganism without the recombinant nucleic acids. Asa result, the sn-2 profile of the cell triglyceride may have greaterthan 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the particular fattyacid.

The identity of the acyl chains located at the distinct stereospecificor regiospecific positions in a glycerolipid can be evaluated throughone or more analytical methods known in the art (see Luddy et al., J.Am. Oil Chem. Soc., 41, 693-696 (1964), Brockerhoff, J. Lipid Res., 6,10-15 (1965), Angers and Aryl, J. Am. Oil Chem. Soc.,Vol. 76:4, (1999),Buchgraber et al., Eur. J. Lipid Sci. Technol., 106, 621-648 (2004)), orin accordance with Examples 1, 2, and 8 given below.

The positional distribution of fatty acids in a triglyceride moleculecan be influenced by the substrate specificity of acyltransferases andby the concentration and type of available acyl moieties substrate pool.Nonlimiting examples of enzymes suitable for altering theregiospecificity of a triglyceride produced in a recombinantmicroorganism are listed in Tables 1-4. One of skill in the art mayidentify additional suitable proteins.

TABLE 1 Glycerol-3-phosphate acyltransferases and GenBank accessionnumbers. glycerol-3-phosphate Arabidopsis BAA00575 acyltransferasethaliana glycerol-3-phosphate Chlamydomonas EDP02129 acyltransferasereinhardtii glycerol-3-phosphate Chlamydomonas Q886Q7 acyltransferasereinhardtii acyl-(acyl-carrier-protein): Cucurbita BAB39688glycerol-3-phosphate moschata acyltransferase glycerol-3-phosphateElaeis AAF64066 acyltransferase guineensis glycerol-3-phosphate GarcinaABS86942 acyltransferase mangostana glycerol-3-phosphate GossypiumADK23938 acyltransferase hirsutum glycerol-3-phosphate Jatropha ADV77219acyltransferase curcas plastid glycerol-3- Jatropha ACR61638 phosphateacyltransferase curcas plastidial glycerol- Ricinus EEF43526 phosphateacyltransferase communis glycerol-3-phosphate Vica faba AAD05164acyltransferase glycerol-3-phosphate Zea mays ACG45812 acyltransferase

Lysophosphatidic acid acyltransferases suitable for use with themicrobes and methods of the invention include, without limitation, thoselisted in Table 2.

TABLE 2 Lysophosphatidic acid acyltransferases and GenBank accessionnumbers. 1-acyl-sn-glycerol-3- Arabidopsis AEE85783 phosphateacyltransferase thaliana 1-acyl-sn-glycerol-3- Brassica ABQ42862phosphate acyltransferase juncea 1-acyl-sn-glycerol-3- Brassica ABM92334phosphate acyltransferase juncea 1-acyl-sn-glycerol-3- Brassica CAB09138phosphate acyltransferase napus lysophosphatidic acid ChlamydomonasEDP02300 acyltransferase reinhardtii lysophosphatidic acid LimnanthesAAC49185 acyltransferase alba 1-acyl-sn-glycerol-3- Limnanthes CAA88620phosphate acyltransferase douglasii (putative)acyl-CoA:sn-1-acylglycerol- Limnanthes ABD62751 3-phosphateacyltransferase douglasii 1-acylglycerol-3-phosphate Limnanthes CAA58239O-acyltransferase douglasii 1-acyl-sn-glycerol-3- Ricinus EEF39377phosphate acyltransferase communis

Diacylglycerol acyltransferases suitable for use with the microbes andmethods of the invention include, without limitation, those listed inTable 3.

TABLE 3 Diacylglycerol acyltransferases and GenBank accession numbers.diacylglycerol Arabidopsis CAB45373 acyltransferase thalianadiacylglycerol Brassica AAY40784 acyltransferase juncea putativediacylglycerol Elaeis AEQ94187 acyltransferase guineensis putativediacylglycerol Elaeis AEQ94186 acyltransferase guineensis acylCoA:diacylglycerol Glycine AAT73629 acyltransferase max diacylglycerolHelianthus ABX61081 acyltransferase annus acyl-CoA:diacylglycerol OleaAAS01606 acyltransferase 1 europaea diacylglycerol Ricinus AAR11479acyltransferase communis

Phospholipid diacylglycerol acyltransferases suitable for use with themicrobes and methods of the invention include, without limitation, thoselisted in Table 4.

TABLE 4 Phospholipid diacylglycerol acyltransferases and GenBankaccession numbers. phospholipid:diacylglycerol Arabidopsis AED91921acyltransferase thaliana Putative phospholipid: Elaeis AEQ94116diacylglycerol guineensis acyltransferase phospholipid:diacylglycerolGlycine XP_003541296 acyltransferase 1-like maxphospholipid:diacylglycerol Jatropha AEZ56255 acyltransferase curcasphospholipid:diacylglycerol Ricinus ADK92410 acyltransferase communisphospholipid:diacylglycerol Ricinus AEW99982 acyltransferase communis

In an embodiment of the invention, known or novel LPAAT genes aretransformed into the oleaginous cells so as to alter the fatty acidprofile of triglycerides produced by those cells, most notably byaltering the sn-2 profile of the triglycerides. For example, by virtueof expressing an exogenous active LPAAT in an oleaginous cell, thepercent of unsaturated fatty acid at the sn-2 position is increased by10, 20, 30, 40, 50, 60, 70, 80, 90% or more. For example, a cell mayproduce triglycerides with 30% unsaturates (which may be primarily 18:1and 18:2 and 18:3 fatty acids) at the sn-2 position. In this example,introduction of the LPAAT activity increases the unsaturates at the sn-2position by 20% so that 36% of the triglycerides comprise unsaturates atthe sn-2 position. Alternately, an exogenous LPAAT can be used toincrease mid-chain fatty acids including saturated mid-chains such asC8:0, C10:0, C12:0, C14:0 or C16:0 moieties at the sn-2 position. As aresult, mid-chain levels in the overall fatty acid profile may beincreased. Examples 43 and 44 describe altering the sn-2 and fatty acidprofiles in an oleaginous microbe. As can be seen from those examples,the choice of LPAAT gene is important in that different LPAATs can causea shift in the sn-2 and fatty acid profiles toward different acyl groupchain-lengths or saturation levels. For example, the LPAAT of Example 43increases C10-C14 fatty acids and the LPAAT of Example 44 causes anincrease in C16 and C18 fatty acids. As in these examples, introductionof an exogenous LPAAT can be combined with introduction of exogenousacyl-ACP thioesterase. Combining a mid-chain preferring LPAAT and amid-chain preferring FatB was found to give an additive effect; thefatty acid profile was shifted more toward the mid-chain fatty acidswhen both an exogenous LPAAT and FatB gene was present than when only anexogenous FatB gene was present. In a specific embodiment, the oilproduced by a cell comprising an exogenous mid-chain specific LPAAT and(optionally) an exogenous FatB acyl-ACP thioesterase gene can have afatty acid profile with 40, 50, 60, 70, 80% or more of C8:0, C10:0,C12:0, C14:0, or C16:0 fatty acids (separately or in sum).

Specific embodiments of the invention are a nucleic acid construct, acell comprising the nucleic acid construct, a method of cultivating thecell to produce a triglyceride, and the triglyceride oil produced wherethe nucleic acid construct has a promoter operably linked to a novelLPAAT coding sequence. The coding sequence can have an initiation codonupstream and a termination codon downstream followed by a 3 UTRsequence. In a specific embodiment, the LPAAT gene has LPAAT activityand a coding sequence have at least 75, 80, 85, 90, 95, 96, 97, 98, or99% sequence identity to any of the cDNAs of SEQ ID NOs: 80 to 85 or afunctional fragment thereof including equivalent sequences by virtue ofdegeneracy of the genetic code. Introns can be inserted into thesequence as well. Alternately, the LPAAT gene codes for the amino acidsequence of SEQ ID NOs 77-79 or functional fragments thereof, or aprotein having at least 75, 80, 85, 90, 95, 96, 97, 98, or 99% aminoacid sequence identity . In addition to microalgae and other oleaginouscells, plants expressing the novel LPAAT as transgenes are expresslyincluded in the embodiments and can be produced using known geneticengineering techniques.

VI. CELLS WITH EXOGENOUS ELONGASES OR ELONGASE COMPLEX ENZYMES

In various embodiments of the present invention, one or more genesencoding elongases or components of the fatty acyl-CoA elongationcomplex can be introduced into an oleaginous cell (e.g., a plastidicmicroalgal cell) so as to alter the fatty acid composition of the cellor of a cell oil produced by the cell. The genes may encode abeta-ketoacyl-CoA synthase (also referred to as 3-ketoacyl synthase,beta-ketoacyl synthase or KCS), a ketoacyl-CoA reductase, ahydroxyacyl-CoA dehydratase, enoyl-CoA reductase, or elongase. Theenzymes encoded by these genes are active in the elongation of acyl-coAmolecules liberated by acyl-ACP thioesterases. Recombinant nucleic acidsmay be integrated into a plasmid or chromosome of the cell. In aspecific embodiment, the cell is of Chlorophyta, including heterotrophiccells such as those of the genus Prototheca.

Beta-Ketoacyl-CoA synthase and elongase enzymes suitable for use withthe microbes and methods of the invention include, without limitation,those listed in Table 5.

TABLE 5 Beta-Ketoacyl-CoA synthases and elongases listed with GenBankaccession numbers. Trypanosoma brucei elongase 3 (GenBank Accession No.AAX70673), Marchanita polymorpha (GenBank Accession No. AAP74370),Trypanosoma cruzi fatty acid elongase, putative (GenBank Accession No.EFZ33366), Nannochloropsis oculata fatty acid elongase (GenBankAccession No. ACV21066.1), Leishmania donovani fatty acid elongase,putative (GenBank Accession No. CBZ32733.1), Glycine max 3-ketoacyl-CoAsynthase 11-like (GenBank Accession No. XP_003524525.1), Medicagotruncatula beta-ketoacyl-CoA synthase (GenBank Accession No.XP_003609222), Zea mays fatty acid elongase (GenBank Accession No.ACG36525), Gossypium hirsutum beta- ketoacyl-CoA synthase (GenBankAccession No. ABV60087), Helianthus annuus beta-ketoacyl-CoA synthase(GenBank Accession No. ACC60973.1), Saccharomyces cerevisiae ELO1(GenBank Accession No. P39540), Simmondsia chinensis beta- ketoacyl-CoAsynthase (GenBank Accession No. AAC49186), Tropaeolum majus putativefatty acid elongase (GenBank Accession No. AAL99199, Brassica napusfatty acid elongase (GenBank Accession No. AAA96054)

In an embodiment of the invention, an exogenous gene encoding abeta-ketoacyl-CoA synthase or elongase enzyme having preferentialspecificity for elongating an acyl substrate comprising a specificnumber of carbon atoms and/or a specific degree of acyl chain saturationis introduced into a oleaginous cell so as to produce a cell or an oilenriched in fatty acids of specified chain length and/or saturation.Example 40 describes engineering of Prototheca strains in whichexogenous fatty acid elongases with preferences for extending midchainfatty acyl-CoAs have been overexpressed to increase the concentration ofstearate. Examples 42 and 54 describe engineering of Prototheca in whichexogenous elongases or beta-ketoacyl-CoA synthases with preferences forextending monounsaturated and saturated C18- and C20-CoA substrates areoverexpressed to increase the concentration of erucic acid.

In specific embodiments, the oleaginous cell produces an oil comprisinggreater than 0.5, 1, 2, 5, 10, 20, 30, 40, 50, 60 70, or 80% erucicand/or eicosenoic acid. Alternately, the cell produces an oil comprising0.5-5, 5-10, 10-15, 15-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80,80-90, or 90-99% erucic or eicosenoic acid. The cell may compriserecombinant acids described above in connection with high-oleic oilswith a further introduction of an exogenous beta-ketoacyl-CoA synthasethat is active in elongating oleoyl-CoA. As a result of the expressionof the exogenous beta-ketoacyl-CoA synthase, the natural production oferucic or eicosenoic acid by the cell can be increased by more than 2,3, 4, 5, 10, 20, 30, 40, 50, 70, 100, 130, 170 or 200 fold. The higherucic and/or eicosenoic oil can also be a high stability oil; e.g., onecomprising less than 5, 4, 3, 2, or 1% polyunsaturates and/or having theOSI values described in Section IV or this application and accompanyingExamples. In a specific embodiment, the cell is a microalgal cell,optionally cultivated heterotrophically. As in the other embodiments,the oil/fat can be produced by genetic engineering of a plastidic cell,including heterotrophic microalgae of the phylum Chlorophyta, the classTrebouxiophytae, the order Chlorellales, or the family Chlorellacae.Preferably, the cell is oleaginous and capable of accumulating at least40% oil by dry cell weight. The cell can be an obligate heterotroph,such as a species of Prototheca, including Prototheca moriformis orPrototheca zopfii.

In specific embodiments, an oleaginous microbial cell, optionally anoleaginous microalgal cell, optionally of the phylum Chlorophyta, theclass Trebouxiophytae, the order Chlorellales, or the familyChlorellacae expresses an enzyme having 80, 85, 90, 95, 96, 97, 98, or99% amino acid sequence identity to an enzyme of Table 5.

VII. REGIOSPECIFIC AND STEREOSPECIFIC OILS/FATS

In an embodiment, a recombinant cell produces a cell fat or oil having agiven regiospecific makeup. As a result, the cell can producetriglyceride fats having a tendency to form crystals of a givenpolymorphic form; e.g., when heated to above melting temperature andthen cooled to below melting temperature of the fat. For example, thefat may tend to form crystal polymorphs of the β or β′ form (e.g., asdetermined by X-ray diffraction analysis), either with or withouttempering. The fats may be ordered fats. In specific embodiments, thefat may directly from either β or β′ crystals upon cooling;alternatively, the fat can proceed through a β form to a β′ form. Suchfats can be used as structuring, laminating or coating fats for foodapplications. The cell fats can be incorporated into candy, dark orwhite chocolate, chocolate flavored confections, ice cream, margarinesor other spreads, cream fillings, pastries, or other food products.Optionally, the fats can be semi-solid (at room temperature) yet free ofartificially produced trans-fatty acids. Such fats can also be useful inskin care and other consumer or industrial products.

As in the other embodiments, the fat can be produced by geneticengineering of a plastidic cell, including heterotrophic eukaryoticmicroalgae of the phylum Chlorophyta, the class Trebouxiophytae, theorder Chlorellales, or the family Chlorellacae. Preferably, the cell isoleaginous and capable of accumulating at least 40% oil by dry cellweight. The cell can be an obligate heterotroph, such as a species ofPrototheca, including Prototheca moriformis or Prototheca zopfii. Thefats can also be produced in autotrophic algae or plants. Optionally,the cell is capable of using sucrose to produce oil and a recombinantinvertase gene may be introduced to allow metabolism of sucrose, asdescribed in PCT Publications WO2008/151149, WO2010/06032,WO2011/150410, WO2011/150411, and international patent applicationPCT/US12/23696. The invertase may be codon optimized and integrated intoa chromosome of the cell, as may all of the genes mentioned here. It hasbeen found that cultivated recombinant microalgae can produce hardstockfats at temperatures below the melting point of the hardstock fat. Forexample, Prototheca moriformis can be altered to heterotrophicallyproduce triglyceride oil with greater than 50% stearic acid attemperatures in the range of 15 to 30° C., wherein the oil freezes whenheld at 30° C.

In an embodiment, the cell fat has at least 30, 40, 50, 60, 70, 80, or90% fat of the general structure [saturated fatty acid(sn-1)-unsaturated fatty acid (sn-2)-saturated fatty acid (sn-3)]. Thisis denoted below as Sat-Unsat-Sat fat. In a specific embodiment, thesaturated fatty acid in this structure is preferably stearate orpalmitate and the unsaturated fatty acid is preferably oleate. As aresult, the fat can form primarily β or β′ polymorphic crystals, or amixture of these, and have corresponding physical properties, includingthose desirable for use in foods or personal care products. For example,the fat can melt at mouth temperature for a food product or skintemperature for a cream, lotion or other personal care product (e.g., amelting temperature of 30 to 40, or 32 to 35° C.). Optionally, the fatscan have a 2 L or 3L lamellar structure (e.g., as determined by X-raydiffraction analysis). Optionally, the fat can form this polymorphicform without tempering.

In a specific related embodiment, a cell fat triglyceride has a highconcentration of SOS (i.e. triglyceride with stearate at the terminalsn-1 and sn-3 positions, with oleate at the sn-2 position of theglycerol backbone). For example, the fat can have triglyceridescomprising at least 50, 60, 70, 80 or 90% SOS. In an embodiment, the fathas triglyceride of at least 80% SOS. Optionally, at least 50, 60, 70,80 or 90% of the sn-2 linked fatty acids are unsaturated fatty acids. Ina specific embodiment, at least 95% of the sn-2 linked fatty acids areunsaturated fatty acids. In addition, the SSS (tri-stearate) level canbe less than 20, 10 or 5% and/or the C20:0 fatty acid (arachidic acid)level may be less than 6%, and optionally greater than 1% (e.g., from 1to 5%). For example, in a specific embodiment, a cell fat produced by arecombinant cell has at least 70% SOS triglyceride with at least 80%sn-2 unsaturated fatty acyl moieties. In another specific embodiment, acell fat produced by a recombinant cell has TAGs with at least 80% SOStriglyceride and with at least 95% sn-2 unsaturated fatty acyl moieties.In yet another specific embodiment, a cell fat produced by a recombinantcell has TAGs with at least 80% SOS, with at least 95% sn-2 unsaturatedfatty acyl moieties, and between 1 to 6% C20 fatty acids.

In yet another specific embodiment, the sum of the percent stearate andpalmitate in the fatty acid profile of the cell fat is twice thepercentage of oleate, ±10, 20, 30 or 40% [e.g., (% P+% S)/%O=2.0±20%].Optionally, the sn-2 profile of this fat is at least 40%, and preferablyat least 50, 60, 70, or 80% oleate (at the sn-2 position). Alsooptionally, this fat may be at least 40, 50, 60, 70, 80, or 90% SOS.Optionally, the fat comprises between 1 to 6% C20 fatty acids.

In any of these embodiments, the high SatUnsatSat fat may tend to formβ′ polymorphic crystals. Unlike previously available plant fats likecocoa butter, the SatUnsatSat fat produced by the cell may form β′polymorphic crystals without tempering. In an embodiment, the polymorphforms upon heating to above melting temperature and cooling to less thatthe melting temperature for 3, 2, 1, or 0.5 hours. In a relatedembodiment, the polymorph forms upon heating to above 60° C. and coolingto 10° C. for 3, 2, 1, or 0.5 hours.

In various embodiments the fat forms polymorphs of the β form, β′ form,or both, when heated above melting temperature and the cooled to belowmelting temperature, and optionally proceeding to at least 50% ofpolymorphic equilibrium within 5, 4, 3, 2, 1, 0.5 hours or less whenheated to above melting temperature and then cooled at 10° C. The fatmay form β′ crystals at a rate faster than that of cocoa butter.

Optionally, any of these fats can have less than 2 mole %diacylglycerol, or less than 2 mole % mono and diacylglycerols, in sum.

In an embodiment, the fat may have a melting temperature of between30-60° C., 30-40° C., 32 to 37° C., 40 to 60° C. or 45 to 55° C. Inanother embodiment, the fat can have a solid fat content (SFC) of 40 to50%, 15 to 25%, or less than 15% at 20° C. and/or have an SFC of lessthan 15% at 35° C.

The cell used to make the fat may include recombinant nucleic acidsoperable to modify the saturate to unsaturate ratio of the fatty acidsin the cell triglyceride in order to favor the formation of SatUnsatSatfat. For example, a knock-out or knock-down of stearoyl-ACP desaturase(SAD) gene can be used to favor the formation of stearate over oleate orexpression of an exogenous mid-chain-preferring acyl-ACP thioesterasegene can increase the levels mid-chain saturates. Alternately a geneencoding a SAD enzyme can be overexpressed to increase unsaturates.

In a specific embodiment, the cell has recombinant nucleic acidsoperable to elevate the level of stearate in the cell. As a result, theconcentration of SOS may be increased. Example 9 demonstrates that theregiospecific profile of the recombinant microbe is enriched for theSatUnsatSat triglycerides POP, POS, and SOS as a result ofoverexpressing a Brassica napus C18:0-preferring thioesterase. Anadditional way to increase the stearate of a cell is to decrease oleatelevels. For cells having high oleate levels (e.g., in excess of one halfthe stearate levels) one can also employ recombinant nucleic acids orclassical genetic mutations operable to decrease oleate levels. Forexample, the cell can have a knockout, knockdown, or mutation in one ormore FATA alleles, which encode an oleate liberating acyl-ACPthioesterase, and/or one or more alleles encoding a stearoyl ACPdesaturase (SAD). Example 35 describes the inhibition of SAD2 geneproduct expression using hairpin RNA to produce a fatty acid profile of37% stearate in Prototheca moriformis (UTEX 1435), whereas the wildtypestrain produced less than 4% stearate, a more than 9-fold improvement.Moreover, while the strains of Example 35 are engineered to reduce SADactivity, sufficient SAD activity remains to produce enough oleate tomake SOS, POP, and POS. See the TAG profiles of Example 47. In specificexamples, one of multiple SAD encoding alleles may be knocked out and/orone or more alleles are downregulated using inhibition techniques suchas antisense, RNAi, or siRNA, hairpin RNA or a combination thereof. Invarious embodiments, the cell can produce TAGs that have 20-30, 30-40,40-50, 50-60, 60-70, 70-80, 80-90, or 90 to about 100% stearate. Inother embodiments, the cells can produce TAGs that are 20-30, 30-40,40-50, 50-60, 60-70, 70-80, 80-90, or 90 to about 100% SOS. Optionally,or in addition to genetic modification, stearoyl ACP desaturase can beinhibited chemically; e.g., by addition of sterculic acid to the cellculture during oil production.

Surprisingly, knockout of a single FATA allele has been found toincrease the presence of C18 fatty acids produced in microalgae. Byknocking out one allele, or otherwise suppressing the activity of theFATA gene product (e.g., using hairpin RNA), while also suppressing theactivity of stearoyl-ACP desaturase (using techniques disclosed herein),stearate levels in the cell can be increased.

Another genetic modification to increase stearate levels includesincreasing a ketoacyl ACP synthase (KAS) activity in the cell so as toincrease the rate of stearate production. It has been found that inmicroalgae, increasing KASII activity is effective in increasing C18synthesis and particularly effective in elevating stearate levels incell triglyceride in combination with recombinant DNA effective indecreasing SAD activity. Recombinant nucleic acids operable to increaseKASII (e.g., an exogenous KasII gene) can be also be combined with aknockout or knockdown of a FatA gene, or with knockouts or knockdowns ofboth a FatA gene and a SAD gene). Optionally, the KASII gene encodes aprotein having at least 75, 80, 85, 90, 95, 96, 97, 98, or 99% aminoacid identity to the KASII Prototheca moriformis (mature protein givenin SEQ ID NO: 161), or any plant KASII gene disclosed herein (e.g., inExample 60) or known in the art including a microalgal KASII.

Optionally, the cell can include an exogenous stearate-liberatingacyl-ACP thioesterase, either as a sole modification or in combinationwith one or more other stearate-increasing genetic modifications. Forexample the cell may be engineered to overexpress an acyl-ACPthioesterase with preference for cleaving C18:0-ACPs. Example 9describes the expression of exogenous C18:0-preferring acyl-ACPthioesterases to increase stearate in the fatty acid profile of themicroalgae, Prototheca moriformis (UTEX 1435), from about 3.7% to about30.4% (over 8-fold). Example 41 provides additional examples ofC18:0-preferring acyl-ACP thioesterases function to elevate C18:0 levelsin Prototheca. Optionally, the stearate-preferring acyl-ACP thioesterasegene encodes an enzyme having at least 80, 85, 90, 91, 92, 93, 94, 95,96, 97, 98 or 9% amino acid identity to the gene products of Example 9or 41 (Seq ID NOS. 28, 65, 67, 69, 71, 73, or 75 omitting FLAG tags whenpresent). Introduction of the acyl-ACP-thioesterase can be combined witha knockout or knockdown of one or more endogenous acyl-ACP thioesterasealleles. Introduction of the thioesterase can also be combined withoverexpression of an elongase (KCS) or beta-ketoacyl-CoA synthase. Inaddition, one or more exogenous genes (e.g., encoding SAD or KASII) canbe regulated via an environmental condition (e.g., by placement inoperable linkage with a regulatable promoter). In a specific example, pHand/or nitrogen level is used to regulate an amt03 promoter. Theenvironmental condition may then be modulated to tune the cell toproduce the desired amount of stearate appearing in cell triglycerides(e.g., to twice the oleate concentration). As a result of thesemanipulations, the cell may exhibit an increase in stearate of at least5, 10, 15, or 20 fold.

As a further modification, alone or in combination with the otherstearate increasing modifications, the cell can comprise recombinantnucleic acids operable to express an elongase or a beta-ketoacyl-CoAsynthase. For example, overexpression of a C18:0-preferring acyl-ACPthioesterases may be combined with overexpression of amidchain-extending elongase or KCS to increase the production ofstearate in the recombinant cell. One or more of the exogenous genes(e.g., encoding a thioesterase, elongase, or KCS) can be regulated viaan environmental condition (e.g., by placement in operable linkage witha regulatable promoter). In a specific example, pH and/or nitrogen levelis used to regulate an amt03 promoter or any of the promoters of example63 including those that are less pH-sensitive than amt03. Theenvironmental condition may then be modulated to tune the cell toproduce the desired amount of stearate appearing in cell triglycerides(e.g., to twice the oleate concentration). As a result of thesemanipulations, the cell may exhibit an increase in stearate of at least5, 10, 15, or 20 fold. In addition to stearate, arachidic, behenic,lignoceric, and cerotic acids may also be produced.

In specific embodiments, due to the genetic manipulations of the cell toincrease stearate levels, the ratio of stearate to oleate in the oilproduced by the cell is 2:1±30% (i.e., in the range of 1.4:1 to 2.6:1),2:1±20% or 2:1±10%.

Alternately, the cell can be engineered to favor formation ofSatUnsatSat where Sat is palmitate or a mixture of palmitate andstearate. In this case introduction of an exogenous palmitate liberatingacyl-ACP thioesterase can promote palmitate formation. In thisembodiment, the cell can produce triglycerides, that are at least 30,40, 50, 60, 70, or 80% POP, or triglycerides in which the sum of POP,SOS, and POS is at least 30, 40, 50, 60, 70, 80, or 90% of celltriglycerides. In other related embodiments, the POS level is at least30, 40, 50, 60, 70, 80, or 90% of the triglycerides produced by thecell.

In a specific embodiment, the melting temperature of the oil is similarto that of cocoa butter (about 30-32° C.). The POP, POS and SOS levelscan approximate cocoa butter at about 16, 38, and 23% respectively. Forexample, POP can be 16%±20%, POS can be 38%±20%, and SOS can be 23%±20%.Or, POP can be 16%±15%, POS can be 38%±15%, an SOS can be 23%±15%. Or,POP can be 16%±10%, POS can be 38%±10%, an SOS can be 23%±10%.

As a result of the recombinant nucleic acids that increase stearate, aproportion of the fatty acid profile may be arachidic acid. For example,the fatty acid profile can be 0.01% to 5%, 0.1 to 4%, or 1 to 3%arachidic acid. Furthermore, the regiospecific profile may have 0.01% to4%, 0.05% to 3%, or 0.07% to 2% AOS, or may have 0.01% to 4%, 0.05% to3%, or 0.07% to 2% AOA. It is believed that AOS and AOA may reduceblooming and fat migration in confection comprising the fats of thepresent invention, among other potential benefits.

In addition to the manipulations designed to increase stearate and/orpalmitate, and to modify the SatUnsatSat levels, the levels ofpolyunsaturates may be suppressed, including as described above byreducing delta 12 fatty acid desaturase activity (e.g., as encoded by aFad gene) and optionally supplementing the growth medium or regulatingFAD expression. It has been discovered that, in microalgae (as evidencedby work in Prototheca strains), polyunsaturates are preferentially addedto the sn-2 position. Thus, to elevate the percent of triglycerides witholeate at the sn-2 position, production of linoleic acid by the cell maybe suppressed. The techniques described herein, in connection withhighly oxidatively stable oils, for inhibiting or ablating fatty aciddesaturase (FAD) genes or gene products may be applied with good effecttoward producing SatUnsatSat oils by reducing polyunsaturates at thesn-2 position. As an added benefit, such oils can have improvedoxidatively stability. As also described herein, the fats may beproduced in two stages with polyunsaturates supplied or produced by thecell in the first stage with a deficit of polyunsaturates during the fatproducing stage. The fat produced may have a fatty acid profile havingless than or equal to 15,10,7, 5, 4, 3, 2, 1, or 0.5% polyunsaturates.In a specific embodiment, the oil/fat produced by the cell has greaterthan 50% SatUnsatSat, and optionally greater than 50% SOS, yet has lessthan 3% polyunsaturates. Optionally, polyunsaturates can be approximatedby the sum of linoleic and linolenic acid area% in the fatty acidprofile.

In an embodiment, the cell fat is a Shea stearin substitute having 65%to 95% SOS and optionally 0.001 to 5% SSS. In a related embodiment, thefat has 65% to 95% SOS, 0.001 to 5% SSS, and optionally 0.1 to 8%arachidic acid containing triglycerides. In another related embodiment,the fat has 65% to 95% SOS and the sum of SSS and SSO is less than 10%or less than 5%.

The cell's regiospecific preference can be learned using the analyticalmethod described below (Examples 1-2, 8). Despite balancing thesaturates and unsaturates as describe above, it is possible that thecell enzymes do not place the unsaturated fatty acid at the sn-2position. In this case, genetic manipulations can confer the desiredregiospecificity by (i) reducing the activity of endogenous sn-2specific acyl transferases (e.g., LPAAT) and/or (ii) introducing anexogenous LPAAT with the desired specificity (i.e., introduction ofoleate at sn-2). Where an exogenous LPAAT is introduced, preferably thegene encoding the LPAAT is integrated into a host chromosome and istargeted to the endoplasmic reticulum. In some cases, the host cell mayhave both specific and non-specific LPAAT alleles and suppressing theactivity of one of these alleles (e.g., with a gene knockout) willconfer the desired specificity. For example, genes encoding the LPAATsof SEQ ID NO: 78 and SEQ ID NO: 79 or an LPAAT comprising at least 90,95, 98, or 99% amino acid identity to either of these sequences, or afunctional fragment thereof, can be used to add oleate to the sn-2position in order to boost the levels of SatUnsatSat TAGs. The genes canhave at least 80, 85, 90, 95, 96, 97, 98, or 99% nucleotide identity toany of SEQ ID NOs: 80 to 85 or equivalent sequences by virtue of thedegeneracy of the genetic code. Alternatively, the proteins encoded bythe genes can have at least 80, 85, 90, 95, 96, 97, 98, or 99%nucleotide identity to the gene products of any of SEQ ID NOs: 80 to 85.These genes can be manifest as recombinant nucleic acid constructs,vectors, chromosomes or host cells comprising these sequences orfunctional fragments thereof, which can be found by systematic deletionof nucleic acid from the sequences using known techniques. As a resultof expression of the genes, the amount of sat-unsat-sat TAGs such asSOS, POS, POP, or triglycerides with C8 to C16 fatty acids at the sn-2position can be increased in a host cell.

Among other discoveries, the above discussion and Examples belowhighlight certain pathways to obtain high Sat-Unsat-Sat oils in generaland SOS oils in particular in microorganisms or in plants. Thus, it ispossible that the use of genetic engineering techniques, optionallycombined with classical mutagenesis and breeding, a microalga or higherplant can be produced with an increase in the amount of SatUnsatSat orSOS produced of at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, ormore relative to the starting strain. In another aspect, the SatUnsatSator SOS concentration of a species for which the wild-type produces lessthan 20%, 30%, 40% or 50% SatUnsatSat or SOS can be increased so thatthe SatUnsatSat or SOS is increased to at least 30%, 40%, 50% or 60%,respectively. The key changes, relative to the starting or wild-typeorganism, are to increase the amount of stearate (e.g., by reducing theamount of oleate formed from stearate, e.g., by reducing SAD activity,and/or increasing the amount of palmitate that is converted to stearateby reducing the activity of FATA and/or increasing the activity ofKASII) and by decreasing the amount of linoleate by reducing FAD2/FADcactivity.

Optionally, the starting organism can have triacylglycerol (TAG)biosynthetic machineries which are predisposed toward the synthesis ofTAG species in which oleate or unsaturated fatty acids, predominate atthe sn-2 position. Many oilseed crops have this characteristic. It hasbeen demonstrated that lysophosphatidic acyltransferases (LPAATs) play acritical role in determining the species of fatty acids which willultimately be inserted at the sn-2 position. Indeed, manipulation,through heterologous gene expression, of LPAATs in higher plant seeds,can alter the species of fatty acid occupying the sn-2 position.

One approach to generating oils with significant levels of so-calledstructuring fats (typically comprised of the speciesSOS-stearate-oleate-stearate, POS-palmitate-oleate-stearate, orPOP-palmitate-oleate-palmitate) in agriculturally important oilseeds andin algae, is through the manipulation of endogenous as well asheterologous LPAAT expression. Expression of LPAATs from seedscontaining high levels of structuring fats, for example, would be onestrategy to increase the level of structuring fats in an oil seed oroleaginous algae that normally contains only limited quantities of suchfats.

An alternative or supplementary strategy, however, is to take advantageof the innate propensity of LPAATs in agriculturally important oilseeds(eg, safflower-Carthamus sp., sunflower-Helianthus sp., canola-Brassicasp., peanut-Arachis sp., soybean-Glycine sp., corn-Zea sp., olive-Oleasp., flax-Linum sp., palm-Elaeis sp. and cotton-Gossypium sp., seerepresentative profiles in Table 5a below) and through either geneticengineering alone or a combination of genetic engineering and classicalstrain improvement (i.e. mutagenesis) selectively manipulate the speciesof fatty acids present in order to increase the levels of structuringfats. In the case of SOS, these manipulations are comprised of a seriesof discrete steps, which can be carried out independently. Theseinclude:

Increasing the level of stearate. This can be achieved, as we havedemonstrated in microalgae here and others have shown in higher plants,through the expression of stearate specific FATA activities or downregulation of the endogenous SAD activity; e.g., through direct geneknockout, RNA silencing, or mutation, including classical strainimprovement. Simply elevating stearate levels alone, by the aboveapproaches,however, will not be optimal. For example, in the case ofpalm oil, the already high levels of palmitate, coupled with increasedstearate levels, will likely overwhelm the existing LPAAT activity,leading to significant amounts of stearate and palmitate incorporationinto tri-saturated fatty acids (SSS, PPP, SSP, PPS etc.). Hence, stepsmust be taken to control palmitate levels as well.

Palmitate levels must be minimized in order to create high SOScontaining fats because palmitate, even with a high-functioning LPAAT,will occupy sn-1 or sn-3 positions that could be taken up by stearate,and, as outlined above, too many saturates will result in significantlevels of tri-saturated TAG species. Palmitate levels can be lowered.for example, through down-regulation of endogenous FATA activity throughmutation/classical strain improvement, gene knockouts or RNAi-mediatedstrategies, in instances wherein the endogenous FATA activity hassignificant palmitate activity. Alternatively, or in concert with theabove, palmitate levels can be lowered through over expression ofendogenous KASII activity or classical strain improvement efforts whichmanifest in the same effect, such that elongation from palmitate tostearate is enhanced. Simply lowering palmitate levels via the abovemethods may not be sufficient, however. Take again the example of palmoil. Reduction of palmitate and elevation of stearate via the previousmethods would still leave significant levels of linoleic acid. Theendogenous LPAAT activity in most higher plants species while they willpreferentially insert oleate in the sn-2 position, will insert linoleicas the next most preferred species. As oleate levels decrease, linoleicwill come to occupy the sn-2 position with increased frequency. TAGspecies with linoleic at the sn-2 position have poor structuringproperties as the TAGs will tend to display much higher meltingtemperatures than what is desired in a structuring fat. Hence, increasesin stearate and reductions in palmitate must in turn be balanced byreductions in levels of linoleic fatty acids.

In turn, levels of linoleic fatty acids must be minimized in order tocreate high SOS-containing fats because linoleate, even with a highfunctioning LPAAT will occupy sn-2 positions to the exclusion of oleate,creating liquid oils as opposed to the desired solid fat (at roomtemperature). Linoleate levels can be lowered, as we have demonstratedin microalgae and others have shown in plant oilseeds, through downregulation of endogenous FAD2 desaturases; e.g., throughmutation/classical strain improvement, FAD2 knockouts or RNAi mediateddown regulation of endogenous FAD2 activity. Accordingly, the linoleicacid level in the fatty acid profile can be reduced by at least 10, 20,30, 40, 50, 100, 200, or 300%. For example, an RNAi construct with atleast 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99% identity to thosedisclosed herein can be used to downregulate FAD2.

Although one can choose a starting strain with such an sn-2 preferenceone can also introduce an exogenous LPAAT gene having a greater oleatepreference, to further boost oleate at the sn-2 position and to furtherboost Sat-Unsat-Sat in the TAG profile. Optionally, one can replace oneor more endogenous LPAAT alleles with the exogenous, more specificLPAAT.

The cell oils resulting from the SatUnsatSat/SOS producing organisms canbe distinguished from conventional sources of SOS/POP/POS in that thesterol profile will be indicative of the host organism asdistinguishable from the conventional source. Conventional sources ofSOS/POP/POS include cocoa, shea, mango, sal, illipe, kokum, andallanblackia. See section XII of this disclosure for a discussion ofmicroalgal sterols.

TABLE 5a The fatty acid profiles of some commercial oilseed strains.Common Food Oils* C12:0 C14:0 C16:0 C16:1 C18:0 C18:1 C18:2 C18:3 Cornoil <1.0  8.0-19.0 <0.5 0.5-4.0 19-50 38-65 <2.0 (Zea mays) Cottonseedoil <0.1 0.5-2.0 17-29 <1.5 1.0-4.0 13-44 40-63 0.1-2.1 (Gossypiumbarbadense) Canola <0.1 <0.2 <6.0 <1.0 <2.5 >50 <40 <14 (Brassica rapa,B. napus, B. juncea) Olive <0.1  6.5-20.0 ≤3.5 0.5-5.0 56-85  3.5-20.0≤1.2 (Olea europea) Peanut <0.1 <0.2  7.0-16.0 <1.0 1.3-6.5 35-7213.0-43   <0.6 (Arachis hypogaea) Palm 0.5-5.9 32.0-47.0 2.0-8.0 34-44 7.2-12.0 (Elaeis guineensis) Safflower <0.1 <1.0  2.0-10.0 <0.5 1.0-10.0  7.0-16.0 72-81 <1.5 (Carthamus tinctorus) Sunflower <0.1 <0.5 3.0-10.0 <1.0  1.0-10.0 14-65 20-75 <0.5 (Helianthus annus) Soybean<0.1 <0.5  7.0-12.0 <0.5 2.0-5.5 19-30 48-65  5.0-10.0 (Glycine max)Solin-Flax <0.1 <0.5  2.0-9.0 <0.5 2.0-5.0 8.0-60  40-80 <5.0 (Linumusitatissimum) *Unless otherwise indicated, data taken from the U.S.Pharacopeia's Food and Chemicals Codex, 7th Ed. 2010-2011**

Accordingly, in an embodiment of the present invention, there is amethod for increasing the amount of SOS in an oil (i.e. oil or fat)produced by a cell. The method comprises providing a cell and usingclassical and/or genetic engineering techniques (e.g., mutation,selection, strain-improvement, introduction of an exogenous gene and/orregulator element, or RNA-level modulation such as RNAi) to (i) increasethe stearate in the oil, (ii) decrease the linoleate in the oil, andoptionally (iii) increase the stereospecificity of the addition ofoleate in the sn-2 position. The step of increasing the stearate cancomprise decreasing desaturation by SAD (e.g., knockout, knockdown oruse of regulatory elements) and increasing the conversion of palmitateto stearate (including overexpression of an endogenous or exogenousKASII and/or knockout or knockdown of FATA). Optionally, an exogenousFATA with greater stearate specificity then an endogenous FATA isexpressed in the cell to increase stearate levels. Here,stearate-specificity of a FATA gene is a measure of the gene product'srate of cleavage of stearate over palmitate. The stearate-specific FATAgene insertion can be combined with a knockdown or knockout of theless-specific endogenous FATA gene. In this way, the ratio of stearateto palmitate can be increased, by 10%, 20%, 30%, 40%, 50%, 100% or more.The step of decreasing the linoleate can be via reduction of FADc/FAD2activity including knockout and/or knockdown . The step of increasingthe oleate at the sn-2 position can comprise expressing an exogenousoleate-preferring LPAAT such as an LPAAT having at least 75, 80, 85, 90,85, 96, 97, 98, or 99% amino acid identity to an LPAAT disclosed herein.

In a specific embodiment, the cell (e.g, an oleaginous microalgal orother plastidic cell) produces an oil enriched in SOS (e.g., at least50% SOS and in some cases 60% SOS). The cell is modified in at leastfour genes: (i) a β-ketoacyl-ACP synthase II (KASII) is overexpressed,(ii) activity of an endogenous FATA acyl-ACP thioesterase is reduced(iii) a stearate-specific FATA acyl-ACP thioesterase is overexpressed,(iii) endogenous SAD activity is decreased, and (iv) endogenous FADactivity is decreased. Example 65 demonstrates this embodiment in aPrototheca moriformis microalga by disrupting the coding region ofendogenous FATA and SAD2 through homologous recombination,overexpressing a β-ketoacyl-ACP synthase II (KASII) gene, and activatingFAD2 RNAi to decrease polyunsaturates.

In another specific embodiment, the cell (e.g, an oleaginous microalgalor other plastidic cell) produces an oil enriched in SOS (e.g., at least50% SOS and in some cases 60% SOS). The cell is modified in at leastfour genes: (i) a β-ketoacyl-ACP synthase II (KASII) is overexpressed,(ii) activity of an endogenous FATA acyl-ACP thioesterase is reduced(iii) a stearate-specific FATA acyl-ACP thioesterase is overexpressed,(iv) endogenous SAD activity is decreased, (v) endogenous FAD activityis decreased and (vi) an exogenous oleate-preferring LPAAT is expressed.See Examples 65 and 66. Optionally, these genes or regulatory elementshave at least 75, 80, 85, 90, 85, 96, 97, 98, or 99% nucleic acid oramino acid identity to a gene or gene-product or regulatory elementdisclosed herein. Optionally, one or more of these genes is undercontrol of a pH-sensitive or nitrogen-sensitive (pH-sensitive orpH-insensitive) promoter such as one having at least 75, 80, 85, 90, 85,96, 97, 98, or 99% nucleic acid identity to one of those disclosedherein. Optionally, the cell oil is fractionated (see Example 64).

In an embodiment, fats produced by cells according to the invention areused to produce a confection, candy coating, or other food product. As aresult, a food product like a chocolate or candy bar may have the “snap”(e.g., when broken) of a similar product produced using cocoa butter.The fat used may be in a beta polymorphic form or tend to a betapolymorphic form. In an embodiment, a method includes adding such a fatto a confection. Optionally, the fat can be a cocoa butter equivalentper EEC regulations, having greater than 65% SOS, less than 45%unsaturated fatty acid, less than 5% polyunsaturated fatty acids, lessthan 1% lauric acid, and less than 2% trans fatty acid. The fats canalso be used as cocoa butter extenders, improvers, replacers, oranti-blooming agents, or as Shea butter replacers, including in food andpersonal care products. High SOS fats produced using the cells andmethods disclosed here can be used in any application or formulationthat calls for Shea butter or Shea fraction. However, unlike Sheabutter, fats produced by the embodiments of the invention can have lowamounts of unsaponifiables; e.g. less than 7, 5, 3, or 2%unsaponifiables. In addition, Shea butter tends to degrade quickly dueto the presence of diacylglycerides whereas fats produced by theembodiments of the invention can have low amounts of diacylglycerides;e.g., less than 5, 4, 3, 2, 1, or 0.5% diacylglycerides.

In an embodiment of the invention there is a cell fat suitable as ashortening, and in particular, as a roll-in shortening. Thus, theshortening may be used to make pastries or other multi-laminate foods.The shortening can be produced using methods disclosed herein forproducing engineered organisms and especially heterotrophic microalgae.In an embodiment, the shortening has a melting temperature of between 40to 60° C. and preferably between 45-55° C. and can have a triglycerideprofile with 15 to 20% medium chain fatty acids (C8 to C14), 45-50% longchain saturated fatty acids (C16 and higher), and 30-35% unsaturatedfatty acids (preferably with more oleic than linoleic). The shorteningmay form β′ polymorphic crystals, optionally without passing through theβ polymorphic form. The shortening may be thixotropic. The shorteningmay have a solid fat content of less than 15% at 35° C. In a specificembodiment, there is a cell oil suitable as a roll-in shorteningproduced by a recombinant microalga, where the oil has a yield stressbetween 400 and 700 or 500 and 600 Pa and a storage modulus of greaterthan 1×10⁵ Pa or 1×10⁶ Pa. (see Example 46)

A structured solid-liquid fat system can be produced using thestructuring oils by blending them with an oil that is a liquid at roomtemperature (e.g., an oil high in tristearin or triolein). The blendedsystem may be suitable for use in a food spread, mayonnaise, dressing,shortening; i.e. by forming an oil-water-oil emulsion. The structuringfats according to the embodiments described here, and especially thosehigh in SOS, can be blended with other oils/fats to make a cocoa butterequivalent, replacer, or extender. For example, a cell fat havinggreater than 65% SOS can be blended with palm mid-fraction to make acocoa butter equivalent.

In general, such high Sat-Unsat-Sat fats or fat systems can be used in avariety of other products including whipped toppings, margarines,spreads, salad dressings, baked goods (e.g. breads, cookies, crackersmuffins, and pastries), cheeses, cream cheese, mayonnaise, etc.

In a specific embodiment, a Sat-Unsat-Sat fat described above is used toproduce a margarine, spread, or the like. For example, a margarine canbe made from the fat using any of the recipes or methods found in U.S.Pat. Nos. 7,118,773, 6,171,636, 4,447,462, 5,690,985, 5,888,575,5,972,412, 6,171,636, or international patent publications WO9108677A1.

In an embodiment, a fat comprises a cell (e.g., from microalgal cells)fat optionally blended with another fat and is useful for producing aspread or margarine or other food product is produced by the geneticallyengineered cell and has glycerides derived from fatty acids whichcomprises:

-   -   (a) at least 10 weight % of C18 to C24 saturated fatty acids,    -   (b) which comprise stearic and/or arachidic and/or behenic        and/or lignoceric acid and    -   (c) oleic and/or linoleic acid, while    -   (d) the ratio of saturated C18 acid/saturated        (C20+C22+C24)-acids ≥1, preferably ≥5, more preferably ≥10,        -   which glycerides contain:    -   (e) ≤5 weight % of linolenic acid calculated on total fatty acid        weight    -   (f) ≤5 weight % of trans fatty acids calculated on total fatty        acid weight    -   (g) ≤75 weight %, preferably ≤60 weight % of oleic acid at the        sn-2 position: which glycerides contain calculated on total        glycerides weight    -   (h) ≤8 weight % HOH+HHO triglycerides    -   (i) ≤5 weight % of trisaturated triglycerides, and optionally        one or more of the following properties:    -   (j) a solid fat content of ≥10% at 10° C.    -   (k) a solid fat content ≤15% at 35° C.,    -   (l) a solid fat content of ≥15% at 10° C. and a solid fat        content ≤25% at 35° C.,    -   (m) the ratio of (HOH+HHO) and (HLH+HHL) triglycerides is >1,        and preferably >2,        -   where H stands for C18-C24 saturated fatty acid, 0 for oleic            acid, and L for linoleic acid.

Optionally, the solid content of the fat (% SFC) is 11 to 30 at 10° C.,4 to 15 at 20° C., 0.5 to 8 at 30° C., and 0 to 4 at 35° C. Alternately,the % SFC of the fat is 20 to 45 at 10° C., 14 to 25 at 20° C., 2 to 12at 30° C., and 0 to 5 at 35° C. In related embodiment, the % SFC of thefat is 30 to 60 at 10° C., 20 to 55 at 20° C., 5 to 35 at 30° C., and 0to 15 at 35° C. The C12-C16 fatty acid content can be <15 weight %. Thefat can have <5 weight % disaturated diglycerides.

In related embodiments there is a spread, margarine or other foodproduct made with the cell oil or cell oil blend. For example, the cellfat can be used to make an edible W/O (water/oil) emulsion spreadcomprising 70-20 wt. % of an aqueous phase dispersed in 30-80 wt. % of afat phase which fat phase is a mixture of 50-99 wt. % of a vegetabletriglyceride oil A and 1-50 wt. % of a structuring triglyceride fat B,which fat consists of 5-100 wt. % of a hardstock fat C and up to 95 wt.% of a fat D, where at least 45 wt. % of the hardstock fat Ctriglycerides consist of SatOSat triglycerides and where Sat denotes afatty acid residue with a saturated C18-C24 carbon chain and O denotesan oleic acid residue and with the proviso that any hardstock fat Cwhich has been obtained by fractionation, hydrogenation, esterificationor interesterification of the fat is excluded. The hardstock fat can bea cell fat produced by a cell according to the methods disclosed herein.Accordingly, the hardstock fat can be a fat having a regiospecificprofile having at least 50, 60, 70, 80, or 90% SOS. The W/O emulsion canbe prepared to methods known in the art including in U.S. Pat. No.7,118,773.

In related embodiment, the cell also expresses an endogenous hydrolyaseenzyme that produces ricinoleic acid. As a result, the oil (e.g., aliquid oil or structured fat) produced may be more easily emulsifiedinto a margarine, spread, or other food product or non-food product. Forexample, the oil produced may be emulsified using no added emulsifiersor using lower amounts of such emulsifiers. The U.S. patent applicationSer. No. 13/365,253 discloses methods for expressing such hydroxylasesin microalgae and other cells. In specific embodiments, a cell oilcomprises at least 1, 2, or 5% SRS, where S is stearate and R isricinoleic acid.

In an alternate embodiment, a cell oil that is a cocoa butter mimetic asdescribed above (or other high sat-unsat-sat oil such as a Shea or Kolummimetic) can be fractionated to remove trisaturates (e.g., tristearinand tripalmitin, SSP, and PPS). For example, it has been found thatmicroalgae engineered to decrease SAD activity to increase SOSconcentration make an oil that can be fractionated to removetrisaturated. See Example 47 and example 64. In specific embodiments,the melting temperature of the fractionated cell oil is similar to thatof cocoa butter (about 30-32° C.). The POP, POS and SOS levels canapproximate cocoa butter at about 16, 38, and 23% respectively. Forexample, POP can be 16%±20%, POS can be 38%±20%, an SOS can be 23%±20%.Or, POP can be 16%±15%, POS can be 38%±15%, an SOS can be 23%±15%. Or,POP can be 16%±10%, POS can be 38%±10%, an SOS can be 23%±10%. Inaddition, the tristearin levels can be less than 5% of thetriacylglycerides.

In an embodiment, a method comprises obtaining a cell oil obtained froma genetically engineered (e.g., microalga or other microbe) cell thatproduces a starting oil with a TAG profile having at least 40, 50, or60% SOS. Optionally, the cell comprises one or more of an overexpressedKASII gene, a SAD knockout or knockdown, or an exogenous C18-preferringFATA gene, an exogenous LPAAT, and a FAD2 knockout or knockdown. The oilis fractionated by dry fractionation or solvent fractionation to give anenriched oil (stearin fraction) that is increased in SOS and decreasedin trisaturates relative to the starting oil. The enriched oil can haveat least 60%, 70% or 80% SOS with no more than 5%, 4%, 3%, 2% or 1%trisaturates. The enriched oil can have a sn-2 profile having 85, 90,95% or more oleate at the sn-2 position. For example, thefractionatedoil can comprise at least 60% SOS, no more than 5% trisaturates and atleast 85% oleate at the sn-2 position. Alternatively, the oil cancomprise at least 70% SOS, no more than 4% trisaturates and at least 90%oleate at the sn-2 position or 80% SOS, no more than 4% trisaturates andat least 95% oleate at the sn-2 position. Optionally, the oil hasessentially identical maximum heat-flow temperatures and/or theDSC-derived SFC curves to Kokum butter. The stearin fraction can beobtained by dry fractionation, solvent fractionation, or a combinationof these. Optionally, the process includes a 2-step dry fractionation ata first temperature and a second temperature. The first termperature canbe higher or lower than the second temperature. In a specificembodiment, the first temperature is effective at removing 00S and thesecond temperature is effective in removing trisaturates. Optionally,the stearin fraction is washed with a solvent (e.g. acetone) to removethe 00S after treatment at the first temperature. Optionally, the firsttemperature is about 24° C. and the second temperature is about 29° C.

VIII. HIGH MID-CHAIN OILS

In an embodiment of the present invention, the cell has recombinantnucleic acids operable to elevate the level of midchain fatty acids(e.g., C8:0, C10:0, C12:0, C14:0, or C16:0 fatty acids) in the cell orin the oil of the cell. One way to increase the levels of midchain fattyacids in the cell or in the oil of the cell is to engineer a cell toexpress an exogenous acyl-ACP thioesterase that has activity towardsmidchain fatty acyl-ACP substrates (e.g., one encoded by a FatB gene),either as a sole modification or in combination with one or more othergenetic modifications. An additional genetic modification to increasethe level of midchain fatty acids in the cell or oil of the cell is theexpression of an exogenous lysophosphatidic acid acyltransferase geneencoding an active lysophosphatidic acid acyltransferase (LPAAT) thatcatalyzes the transfer of a mid-chain fatty-acyl group to the sn-2position of a substituted acylglyceroester. For example, the LPAAT genecan have 75, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% aminoacid sequence identity or have 75, 80, 85 90, 91, 92, 93, 94, 95, 96,97, 98 or 99% nucleic acid sequence identity (or equivalent sequence todegeneracy of the genetic code) to the mid-chain preferring LPAATsdisclosed in Examples 43-44 (SEQ ID NOs 77, 78, 79, 81,82, 84, and 85).In a specific related embodiment, both an exogenous acyl-ACPthioesterase and LPAAT are stably expressed in the cell. In anembodiment, recombinant nucleic acids are introduced into an oleaginouscell (and especially into a plastidic microbial cell) that causeexpression of an exogenous mid-chain-specific thioesterase and anexogenous LPAAT that catalyzes the transfer of a mid-chain fatty-acylgroup to the sn-2 position of a substituted acylglyceroester. As aresult, the cell can be made to increase the percent of a midchain fattyacid in the TAGs that it produces by 10, 20 30, 40, 50, 60, 70, 80,90-fold, or more. Introduction of the exogenous LPAAT can increasemidchain fatty acids at the sn-2 position by 1.2, 1.5, 1.7, 2, 3, 4 foldor more compared to introducing an exogenous mid-chain preferringacyl-ACP thioesterase alone. In an embodiment, the mid-chain fatty acidis greater than 30, 40, 50 60, 70, 80, or 90% of the TAG fatty acidsproduced by the cell. In various embodiments, the mid-chain fatty acidis lauric, myristic, or palmitic. Examples 3, 43, and 44 describeexpression of plant LPAATs in microalgal cells with resultingalterations in fatty acid profiles. As in the examples, the cells canalso express an exogenous acyl-ACP thioesterase (which can also be froma plant) with a preference for a given fatty acyl-ACP chain length. Forexample, a microalgal cell can comprise exogenous genes encoding a LPAATand an acyl-ACP thioesterase that preferentially cleave C8, C10, C12,C14, C8-C12, or C8-C10 fatty acids. In a specific embodiment, such acell is capable of producing a cell oil with a fatty acid profilecomprising 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, or90-99%, >20%, >30%, >40%, >50%, >60%, >70%, >80% or >90% C8, C10, C12,C14, C8-C12, or C8-C10 fatty acids. Other LPAATs can preferentiallycleave C16 or C18 fatty acids (see Example 44). Further geneticmanipulation of the fatty acid desaturase pathway (e.g., as describedinfra) can increase the stability of the oils.

Any of these cell oils can be interesterified. Interesterification can,for example, be used to lower the melting temperature or pour-point ofthe oil. In a specific embodiment, the cell oil comprises at least 50%of the sum of caprylic and capric acids and may be interesterified toreduce the pour point and/or kinematic viscosity. Such an oil (cell orinteresterified) can optionally be a high stability oil comprising, forexample, less than 2% polyunsaturated fatty acids.

Alternately, or in addition to expression of an exogenous LPAAT, thecell may comprise recombinant nucleic acids that are operable to expressan exogenous KASI or KASIV enzyme and optionally to decrease oreliminate the activity of a KASII, which is particularly advantageouswhen a mid-chain-preferring acyl-ACP thioesterase is expressed. Example37 describes the engineering of Prototheca cells to overexpress KASI orKASIV enzymes in conjunction with a mid-chain preferring acyl-ACPthioesterase to generate strains in which production of C10-C12 fattyacids is about 59% of total fatty acids. Mid-chain production can alsobe increased by suppressing the activity of KASI and/or KASII (e.g.,using a knockout or knockdown). Example 38 details the chromosomalknockout of different alleles of Prototheca moriformis (UTEX 1435) KASIin conjunction with overexpression of a mid-chain preferring acyl-ACPthioesterase to achieve fatty acid profiles that are about 76% or 84%C10-C14 fatty acids. Example 39 provides recombinant cells and oilscharacterized by elevated midchain fatty acids as a result of expressionof KASI RNA hairpin polynucleotides. In addition to any of thesemodifications, unsaturated or polyunsaturated fatty acid production canbe suppressed (e.g., by knockout or knockdown) of a SAD or FAD enzyme.

In a particular embodiment, a recombinant cell produces TAG having 40%lauric acid or more. In another related embodiment, a recombinant cellproduces TAG having a fatty acid profile of 40% or more of myristic,caprylic, capric, or palmitic acid. For example, an oleaginousrecombinant clorophyte cell can produce 40% lauric or myristic acid inan oil that makes up 40, 50, or 60% or more of the cell's dry weight.

In a specific embodiment, a recombinant cell comprises nucleic acidsoperable to express a product of an exogenous gene encoding alysophosphatidic acid acyltransferase that catalyzes the transfer of amid-chain fatty-acyl group to the sn-2 position of a substitutedacylglyceroester and nucleic acids operable to express a product of anacyl-ACP thioesterase exogenous gene encoding an active acyl-ACPthioesterase that catalyzes the cleavage of mid-chain fatty acids fromACP. As a result, in one embodiment, the oil produced can becharacterized by a fatty acid profile elevated in C10 and C12 fattyacids and reduced in C16, C18, and C18:1 fatty acids as a result of therecombinant nucleic acids. See Example 3, in which overexpression of aCuphea wrightii acyl-ACP thioesterase and a Cocos nucifera LPAAT geneincreased the percentage of C12 fatty acids from about 0.04% in theuntransformed cells to about 46% and increased the percentage of C10fatty acids from about 0.01% in the untransformed cells to about 11%.For example, the FATB gene can have 75, 80, 85, 90, 91, 92, 93, 94, 95,96, 97, 98 or 99% amino acid sequence identity or have 75, 80, 85 90,91, 92, 93, 94, 95, 96, 97, 98 or 99% nucleic acid sequence identity (orequivalent sequence to degeneracy of the genetic code) to SEQ ID NOs 10or 11. In related embodiments, the increase in midchain fatty acidproduction is greater than 70%, from 75-85%, from 70-90%, from 90-200%,from 200-300%, from 300-400%, from 400-500%, or greater than 500%.

Average chain length can also be reduced by overexpression of aC18-specific acyl-ACP thioesterase. Recombinant nucleic acids operableto overexpress a C18 or other acyl-ACP thioesterase may be used alone orin combination with the other constructs described here to furtherreduce average chain length. Among other uses, the oils produced can beused as cocoa-butter/milk fat substitute. See Example 45 and thediscussion of FIG. 17. In an embodiment, one of the above described highmid-chain producing cells is further engineered to produce a lowpolyunsaturated oil by knocking out or knocking down one or more fattyacyl desaturases, as described above in section IV. Accordingly, the oilproduced can have the high stability characteristic mentioned in thatsection or in corresponding Examples. In a specific embodiment, the cellproduces an oil comprising greater than 30% midchain fatty acids and 5%or less polyunsaturates. In a related embodiment, the cell produces anoil comprising greater than 40% midchain fatty acids and 4% or lesspolyunsaturates. In a further related embodiment, the cell produces anoil comprising greater than 50% midchain fatty acids and 3% or lesspolyunsaturates.

In a specific embodiment, the cell produces an oil characterized by afatty acid profile in which the sum of lauric and myristic acids is atleast 50%, 60% , 70%, or 75%. This can be accomplished using thetechniques of Examples 37-39, 43-44, 52, and 60-61. For example, Example52 describes a method for producing an oil that has a fatty acid profilein which the sum of lauric and myristic acids is about 79% using arecombinant cell with an exogenous plant FATB acyl-ACP thioesterase.

In another specific embodiment, the cell produces a cell oilcharacterized by a fatty acid profile in which capric acid (C10:0) is atleast 30% and lauric acid (C12:0) is at least 30%. For example, theabsolute level of capric acid and lauric acid in the cell oil can bebalanced to within 5, 10, 15, 20 or 30%. This can be accomplished usingthe techniques of Examples 37-39, 43-44, 52, and 60-61. As in Example60, exogenous plant FATB and KASI (or KASIV) genes can be combined togive balanced levels of capric and lauric. Optionally, an endogenousKASI gene can be knocked out and replaced with an exogenous KASI. Inaddition, two or more exogenous FATB genes can be used do reach adesired fatty acid profile. In a specific embodiment, a microalgal cellexpresses at least one and optionally at least two exogenous FATB genesand an exogenous KASI/KASIV gene and produces an extractable cell oilwith at least 30% C10 and at least 30% C12 fatty acids. For example, thecell can express a FATB acyl-ACP thioesterase having at least 70, 75,80, 85, 90 or 95% amino acid sequence identity to the Cuphea hookerianaFATB2 (SEQ ID NO: 158) and a beta-ketoacyl ACP synthase having at least70, 75, 80, 85, 90 or 95% amino acid sequence identity to the Cupheawrightii KASA1 (SEQ ID NO: 159, with alternate transit peptide).Further, a second exogenous FATB gene/enzyme can be expressed. Thesecond FATB can have at least 70, 75, 80, 85, 90 or 95% amino acidsequence identity to the Cuphea wrightii FATB2 acyl-ACP thioesterase(SEQ ID NO: 11.) For these purposes, plastid targeted peptides can bealigned with or with out the plastid targeting transit peptides, whichare less conserved and more easily replaceable than the remaining enzymedomain sequence.

In an embodiment, the cell produces an oil comprising greater than 75%saturated fatty acids. Optionally, the cell produces an oil comprisinggreater than 75% saturated fatty acids with less than 25% capric acid,less than 50% lauric acid, and less than 5% palmitic acid. In relatedembodiments, the oil comprises at least 80%, 95% or 90% saturated fattyacids. Example 60 describes the production of such oil by microalgaecomprising multiple exogenous FATB genes and replacement of anendogenous KASI gene with exogenous KASI or KASIV genes from plants.

Examples 60 and 62 also shows that selection of FATB and KAS genes cangive rise to an oil with at least 50% total saturates with capric andlauric acids balanced to within 20% (or even to within 15%, or 10%).

High-mid chain oils in general, and those produced by strains similar tothose of Example 60 and 62 can possess low kinematic viscosity. Forexample, the oil can have a kinematic viscosity as measured using ASTMD445 at 40° C. of 25 cS±20%, 25 cS±10%, or 25 cS±5%. Likewise, the oilcan have a kinematic viscosity according to ASTM D445 at 100° C. of 5.4cS±20%, 5.4 cS±10%, or 5.4 cS±5%. The oil can have a viscosity index asmeasured using ASTM 2280 of 160±20%, 160±10%, or 160±5%.

In a specific example, an oil prepared using a strain similar to thosereported in Example 60, produced an oil with greater than 30% C10:0 andgreater than 30% C12:0 fatty acids. The oil had a kinematic viscocity byASTM 445 of 24.61 cSt at 40° C. and 5.36 cSt at 100° C. with a viscosityindex (ASTM 2270) of 159. To make this oil, a Cuphea hookeriana FATB2acyl-ACP thioesterase was expressed with a Cuphea wrightii KASA1 gene(with a P. moriformis SAD transit peptide) in Prototheca moriformisunder control of the UAPA1 and AMT03 promoters, respectively. Neomycinresitance was used at the selection marker and the construct withincorporated in the KAS1-1 site. Accordingly, in an embodiment, a hostcell comprises an exogenous gene that expresses a protein having atleast 70, 75, 80, 85, 90, or 95% amino acid sequence identity to SEQ IDNO: 158 and also expresses a protein having at least 70, 75, 80, 85, 90,or 95% amino acid sequence identity to SEQ ID NO: 159. The cell producesan oil comprising at least 30% C10:0 and/or at least 30% C12:0 fattyacids. Optionally, a cell oil can be extracted from the cell that has akinematic viscosity as measured using ASTM D445 at 40° C. of less than30 cSt.

The high mid-chain oils or fatty acids derived from hydrolysis of theseoils may be particularly useful in food, fuel and oleochemicalapplications including the production of lubricants and surfactants. Forexample, fatty acids derived from the cells can be esterified, cracked,reduced to an aldehyde or alcohol, aminated, sulfated, sulfonated, orsubjected to other chemical process known in the art.

In some embodiments, the cell oil is interesterified and the kinematicviscosity of the interesterified cell oil is less than 30, 20, 15, 10,9, 8, 7, 6, 5, 4, 3, 2, or 1 centiStokes at 40° C. In some embodiments,the kinematic viscosity is less than 3 centiStokes at 40° C. In someembodiments, the pour point of an interesterified cell oil is less than,5° C., 0° C., −10° C., −12° C., −15° C., −20° C., −25° C., −30° C., −35°C., −40° C., −45° C., or −50° C. In some embodiments, the pour point isless than −10° C. In some embodiments, the pour point is less than −20°C.

Example 53 describes the use of a plant FatB gene in algae to produceoils in microalgae with greater than 60% myristate. In an embodiment, agene encoding a protein having at least 90, 95, 96, 97, 98, or 99% aminoacid identity to SEQ ID NO:87 or SEQ ID NO:89 is used, optionally incombination with a mid-chain preferred LPAAT as described above.

As described in Example 62, we surprisingly discovered that thecombination of a KASI gene with a FATB gene can shift the fatty acidprofile of an oil produced by the cell in ways that neither gene can doon its own. Specifically, recombinant cells with exogenous plantmyristate-preferring acyl-ACP thioesterases were discovered to shifttheir fatty acid profile to a greater percentage of laurate when a KASIgene was co-expressed. This is unexpected because KASI has an elongaseactivity yet the fatty acid profile was shifted to shorter chains. Inother words, a cell expressing both the exogenous FATB and KASI geneproduced an oil having a fatty acid profile that is shifted towardshorter fatty acid chains than a control cell with the FATB gene butwithout the KASI gene. Accordingly, an embodiment of the inventioncomprises constructing a recombinant cell or using the cell to make anoil, where the cell comprises an exogenous FATB with a givenchain-length preference and a KASI gene, wherein the cell makes an oilwith a shift in distribution toward shorter chains than is obtainedwithout the KASI gene. Optionally, the FATB gene has a nucleic acidsequence that is at least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, or99% identical (or an equivalent sequence by virtue of degeneracy of thegenetic code) or has an amino acid sequence that is least 80, 85, 90,91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to the CcFATB2-UcFATB2FATB of Example 62 (SEQ ID NO: 162), the Cuphea wrightii FATB2 (SEQ IDNO: 11), Cuphea palustris FATB2 (SEQ ID NO: 87; SEQ ID NO: 89), Cupheahyssopifolia FATB1 (SEQ ID NO: 163), Cuphea hyssopifolia FATB3 (SEQ IDNO: 164), or Cuphea hookeriana FATB2 (SEQ ID NO: 158). Optionally, theKASI or KASIV gene has a nucleic acid sequence that is at least 80, 85,90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical (or an equivalentsequence by virtue of degeneracy of the genetic code) or has an aminoacid sequence that is least 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98,or 99% identical to the Cuphea wrightii KASAI of Example 62 (SEQ ID NO:159), the Cuphea hookeriana KASIV encoded by the sequence of SEQ IDNO:49, or the Cuphea pulch. KASIV encoded by SEQ ID NO: 48.

IX. HIGH OLEIC/PALMITIC OIL

In another embodiment, there is a high oleic oil with about 60% oleicacid, 25% palmitic acid and optionally 5% polyunsaturates or less. Thehigh oleic oil can be produced using the methods disclosed in U.S.patent application Ser. No. 13/365,253, which is incorporated byreference in relevant part. For example, the cell can have nucleic acidsoperable to suppress an acyl-ACP thioesterase (e.g., knockout orknockdown of a gene encoding FATA) while also expressing a gene thatincreases KASII activity. The cell can have further modifications toinhibit expression of delta 12 fatty acid desaturase, includingregulation of gene expression as described above. As a result, thepolyunsaturates can be less than or equal to 5, 4, 3, 2, or 1 area%.

X. LOW SATURATE OIL

In an embodiment, a cell oil is produced from a recombinant cell. Theoil produced has a fatty acid profile that has less that 4%, 3%, 2%, or1% (area %), saturated fatty acids. In a specific embodiment, the oilhas 0.1 to 3.5% saturated fatty acids. Certain of such oils can be usedto produce a food with negligible amounts of saturated fatty acids.Optionally, these oils can have fatty acid profiles comprising at least90% oleic acid or at least 90% oleic acid with at least 3%polyunsaturated fatty acids. In an embodiment, a cell oil produced by arecombinant cell comprises at least 90% oleic acid, at least 3% of thesum of linoleic and linolenic acid and has less than 3.5% saturatedfatty acids. In a related embodiment, a cell oil produced by arecombinant cell comprises at least 90% oleic acid, at least 3% of thesum of linoleic and linolenic acid and has less than 3.5% saturatedfatty acids, the majority of the saturated fatty acids being comprisedof chain length 10 to 16. These oils may be produced by recombinantoleaginous cells including but not limited to those described here andin U.S. patent application Ser. No. 13/365,253. For example,overexpression of a KASII enzyme in a cell with a highly active SAD canproduce a high oleic oil with less than or equal to 3.5% saturates.Optionally, an oleate-specific acyl-ACP thioesterase is alsooverexpressed and/or an endogenous thioesterase having a propensity tohydrolyze acyl chains of less than C18 knocked out or suppressed. Theoleate-specific acyl-ACP thioesterase may be a transgene with lowactivity toward ACP-palmitate and ACP-stearate so that the ratio ofoleic acid relative to the sum of palmitic acid and stearic acid in thefatty acid profile of the oil produced is greater than 3, 5, 7, or 10.Alternately, or in addition, a FATA gene may be knocked out or knockeddown, as in Example 36 below. A FATA gene may be knocked out or knockeddown and an exogenous KASII overexpressed. Another optional modificationis to increase KASI and/or KASIII activity, which can further suppressthe formation of shorter chain saturates. Optionally, one or moreacyltransferases (e.g., an LPAAT) having specificity for transferringunsaturated fatty acyl moieties to a substituted glycerol is alsooverexpressed and/or an endogenous acyltransferase is knocked out orattenuated. An additional optional modification is to increase theactivity of KCS enzymes having specificity for elongating unsaturatedfatty acids and/or an endogenous KCS having specificity for elongatingsaturated fatty acids is knocked out or attenuated. Optionally, oleateis increased at the expense of linoleate production by knockout orknockdown of a delta 12 fatty acid desaturase; e.g., using thetechniques of Section IV of this patent application. Optionally, theexogenous genes used can be plant genes; e.g., obtained from cDNAderived from mRNA found in oil seeds.

As described in Example 51, levels of saturated fats may also be reducedby introduction of an exogenous gene (e.g., a plant gene) thatdesaturates palmitic acid to palmitoleic acid. Examples of suitablegenes for use in the oleaginous cells are found in the plants, includingMacfadyena unguis (Cat's claw), Macadamia integrifolia (Macadamia nut)and Hippophae rhamnoides (sea buckthorn). Variant exogenous orendogenous SADs that desaturate palmitoyl-ACP can also be used and arefurther discussed in Example 51. Optionally, the PAD or SAD gene has atleast 95% amino acid sequence identity to the gene product described inExample 51. This modification can be used alone, or in combination witholeate-increasing modifications such as those described immediatelyabove, in section IX and in the Examples, including knockout orknockdown of one or more endogenous FATA alleles and/or overexpressionof KASII. In one embodiment, an oleaginous cell such as an oleaginousmicroalgae has a combination of (i) a FATA knockout or knockdown with(ii) expression of an exogenous PAD gene (this could also be a variantSAD with PAD activity such as a L118W mutant or equivalent, see Examples55-56) and/or a mutation in an endogenous SAD gene to give PAD activity.Such as cell may further comprise an overexpressed endogenous orexogenous KASII gene. In accordance with any of these embodiments of theinvention, the oleaginous cell produces an oil having a fatty acidprofile with 1-2, 2-3, 3-4, 5-6, 7-8, 9-10, 10-15, 15-20, 20-30, 30-40,40-60, 60-70, 70-80, 80-90, or 90-100 area percent palmitoleic acid. Ina specific embodiment, the cell produces greater than 50% oleic acid,greater than 1% palmitoleic acid, and 3.5 area% or less of saturatedfatty acids. In another specific embodiment, a eukaryotic microalgalcell comprises an exogenous gene that desaturates palmitic acid topalmitoleic acid in operable linkage with regulatory elements operablein the microalgal cell. Due to expression and activity of the exogenousgene product, the cell produces a cell oil having a fatty acid profilein which the ratio of palmitoleic acid (C16:1) to palmitic acid (C16:0)is at least 0.05, 0.1 or 0.15, or 0.18. See Example 55 for examples ofcells that produce such oils. Optionally, palmitoleic acid comprises0.5% or more of the profile. Optionally, the cell oil comprises lessthan 3.5% saturated fatty acids.

In addition to the above genetic modifications, the low saturate oil canbe a high-stability oil by virtue of low amounts of polyunsaturatedfatty acids. Methods and characterizations of high-stability,low-polyunsaturated oils are described in the section above entitled LowPolyunsaturated Oils, including method to reduce the activity ofendogenous Δ12 fatty acid desaturase. In a specific embodiment, an oilis produced by a oleaginous microbial cell having a type II fatty acidsynthetic pathway and has no more than 3.5% saturated fatty acids andalso has no more than 3% polyunsaturated fatty acids. In anotherspecific embodiment, the oil has no more than 3% saturated fatty acidsand also has no more than 2% polyunsaturated fatty acids. In anotherspecific embodiment, the oil has no more than 3% saturated fatty acidsand also has no more than 1% polyunsaturated fatty acids. In anotherspecific embodiment, a eukaryotic microalgal cell comprises an exogenousgene that desaturates palmitic acid to palmitoleic acid in operablelinkage with regulatory elements operable in the microalgal cell. Thecell further comprises a knockout or knockdown of a FAD gene. Due to thegenetic modifications, the cell produces a cell oil having a fatty acidprofile in which the ratio of palmitoleic acid (C16:1) to palmitic acid(C16:0) is greater than 0.1, with no more than 3% polyunsaturated fattyacids. Optionally, palmitoleic acid comprises 0.5% or more of theprofile. Optionally, the cell oil comprises less than 3.5% saturatedfatty acids.

The low saturate and low saturate/high stability oil can be blended withless expensive oils to reach a targeted saturated fatty acid level atless expense. For example, an oil with 1% saturated fat can be blendedwith an oil having 7% saturated fat (e.g. high-oleic sunflower oil) togive an oil having 3.5% or less saturated fat.

Oils produced according to embodiments of the present invention can beused in the transportation fuel, oleochemical, and/or food and cosmeticindustries, among other applications. For example, transesterificationof lipids can yield long-chain fatty acid esters useful as biodiesel.Other enzymatic and chemical processes can be tailored to yield fattyacids, aldehydes, alcohols, alkanes, and alkenes. In some applications,renewable diesel, jet fuel, or other hydrocarbon compounds are produced.The present disclosure also provides methods of cultivating microalgaefor increased productivity and increased lipid yield, and/or for morecost-effective production of the compositions described herein. Themethods described here allow for the production of oils from plastidiccell cultures at large scale; e.g., 1000, 10,000, 100,000 liters ormore.

In an embodiment, an oil extracted from the cell has 3.5%, 3%, 2.5%, or2% saturated fat or less and is incorporated into a food product. Thefinished food product has 3.5, 3, 2.5, or 2% saturated fat or less. Forexample, oils recovered from such recombinant microalgae can be used forfrying oils or as an ingredient in a prepared food that is low insaturated fats. The oils can be used neat or blended with other oils sothat the food has less than 0.5 g of saturated fat per serving, thusallowing a label stating zero saturated fat (per US regulation). In aspecific embodiment, the oil has a fatty acid profile with at least 90%oleic acid, less than 3% saturated fat, and more oleic acid thanlinoleic acid.

As with the other oils disclosed in this patent application, thelow-saturate oils described in this section, including those withincreased levels palmitoleic acid, can have a microalgal sterol profileas described in Section XII of this application. For example, viaexpression of an exogenous PAD gene, an oil can be produced with a fattyacid profile characterized by a ratio of palmitoleic acid to palmiticacid of at least 0.1 and/or palmitoleic acid levels of 0.5% or more, asdetermined by FAME GC/FID analysis and a sterol profile characterized byan excess of ergosterol over β-sitosterol and/or the presence of 22,23-dihydrobrassicasterol, poriferasterol or clionasterol.

XI. COCOA BUTTER/MILK-FAT BLEND MIMETICS

In certain embodiments, the cell produces a cell oil that has atemperature-dependent solid fat content (“SFC-curve”) that approximatesa blend of cocoa butter and milk fat. Such oils may be used where thecocoa butter/milk fat blend could be used; for example, in chocolatesother confections, ice cream or other frozen desserts, pastries, ordough, including for quickbreads, or other baked goods. The oils mayinhibit blooming, enhance flavor, enhance texture, or reduce costs. In aspecific example, the cell oil approximates. Accordingly, an embodimentof the invention is using a cell oil from a recombinant microalgal cellto replace a cocoa butter/milk fat blend in a recipe. In a relatedembodiment,

FIG. 17 shows a plot of % solid fat content for various oils as follows(a) P. moriformis RBD oil without lipid pathway engineering, (b)Brazilian cocoa butter+25% milk fat, (c) three replicates of P.moriformis RBD oil from a strain expressing hairpin nucleic acids thatreduce levels of a SAD allele thus reducing oleic acid and increasingstearic acid in the TAG profile, (d) P. moriformis RBD oil from a strainoverexpressing an endogenous OTE (oleoyl acyl-ACP thioesterase, seeExample 45), (e) Malaysian cocoa butter+25% milk fat, and (f) Malaysiancocoa butter. The cocoa butter and cocoa butter milk fat values areliterature values (Bailey's Industrial Oils and Fat Products, 6^(th)ed.)

In an embodiment of the present invention, a cell oil that is similar inthermal properties to a 75% cocoa butter/25% milk fat blend is producedby a microalgal or other cell described above. The cell comprisesrecombinant nucleic acids operable to alter the fatty acid profile oftriglycerides produced by the cell so as that the oil has a solid fatcontent (e.g., as determined by NMR) of 38%±30% at 20° C., 32%±30% at25° C., 17%±30% at 30° C., and less than 5%±30% at 35° C. For the sakeof clarity, ±10% refers to percent of the percent SFC (e.g., 30% of 5%SFC is 1.5% SFC so the range is 3.5 to 6.5% SFC at 35° C.). In relatedembodiments, the oil has a solid fat content (e.g., as determined byNMR) of 38%±20% at 20° C., 32%±20% at 25° C., 17%±20% at 30° C., andless than 5%±20% at 35° C. or the oil has a solid fat content (e.g., asdetermined by NMR) of 38%±10% at 20° C., 32%±10% at 25° C., 17%±10% at30° C., and less than 5%±10% at 35° C.

In a another embodiment a cell high oleic oil produced according to themethods of section IX or corresponding Examples, is converted into astructuring fat such as a cocoa butter equivalent, substitute, extenderby enzymatic interesterification or transesterification with a source ofsaturated fatty acids (e.g. a hardstock fat or saturated fatty acidesters). For example, a 1,3-specific lipase can be used to add stearate,palmitate or both to a high oleic oil having greater than 80% oleicacid.

XII. MINOR OIL COMPONENTS

The oils produced according to the above methods in some cases are madeusing a microalgal host cell. As described above, the microalga can be,without limitation, fall in the classification of Chlorophyta,Trebouxiophyceae , Chlorellales, Chlorellaceae, or Chlorophyceae. It hasbeen found that microalgae of Trebouxiophyceae can be distinguished fromvegetable oils based on their sterol profiles. Oil produced by Chlorellaprotothecoides was found to produce sterols that appeared to bebrassicasterol, ergosterol, campesterol, stigmasterol, and β-sitosterol,when detected by GC-MS. However, it is believed that all sterolsproduced by Chlorella have C24β stereochemistry. Thus, it is believedthat the molecules detected as campesterol, stigmasterol, andβ-sitosterol, are actually 22,23-dihydrobrassicasterol, poriferasteroland clionasterol, respectively. Thus, the oils produced by themicroalgae described above can be distinguished from plant oils by thepresence of sterols with C24β stereochemistry and the absence of C24αstereochemistry in the sterols present. For example, the oils producedmay contain 22, 23-dihydrobrassicasterol while lacking campesterol;contain clionasterol, while lacking in β-sitosterol, and/or containporiferasterol while lacking stigmasterol. Alternately, or in addition,the oils may contain significant amounts of Δ⁷-poriferasterol.

In one embodiment, the oils provided herein are not vegetable oils.Vegetable oils are oils extracted from plants and plant seeds. Vegetableoils can be distinguished from the non-plant oils provided herein on thebasis of their oil content. A variety of methods for analyzing the oilcontent can be employed to determine the source of the oil or whetheradulteration of an oil provided herein with an oil of a different (e.g.plant) origin has occurred. The determination can be made on the basisof one or a combination of the analytical methods. These tests includebut are not limited to analysis of one or more of free fatty acids,fatty acid profile, total triacylglycerol content, diacylglycerolcontent, peroxide values, spectroscopic properties (e.g. UV absorption),sterol profile, sterol degradation products, antioxidants (e.g.tocopherols), pigments (e.g. chlorophyll), d13C values and sensoryanalysis (e.g. taste, odor, and mouth feel). Many such tests have beenstandardized for commercial oils such as the Codex Alimentariusstandards for edible fats and oils.

Sterol profile analysis is a particularly well-known method fordetermining the biological source of organic matter. Campesterol,b-sitosterol, and stigmasterol are common plant sterols, withb-sitosterol being a principle plant sterol. For example, b-sitosterolwas found to be in greatest abundance in an analysis of certain seedoils, approximately 64% in corn, 29% in rapeseed, 64% in sunflower, 74%in cottonseed, 26% in soybean, and 79% in olive oil (Gul et al. J. Celland Molecular Biology 5:71-79, 2006).

Oil isolated from Prototheca moriformis strain UTEX1435 were separatelyclarified (CL), refined and bleached (RB), or refined, bleached anddeodorized (RBD) and were tested for sterol content according to theprocedure described in JAOCS vol. 60, no. 8, August 1983. Results of theanalysis are shown below (units in mg/100 g) in Table 5b.

TABLE 5b Sterol profiles of oils from UTEX 1435. Refined, Clari- Refined& bleached, & Sterol Crude fied bleached deodorized 1 Ergosterol 384  398   293   302    (56%)  (55%)  (50%)  (50%) 2 5,22-cholestadien-24-14.6 18.8 14   15.2 methyl-3-ol (2.1%) (2.6%) (2.4%) (2.5%)(Brassicasterol) 3 24-methylcholest-5- 10.7 11.9 10.9 10.8 en-3-ol(Campersterol (1.6%) (1.6%) (1.8%) (1.8%) or 22,23-dihydrobrassicasterol) 4 5,22-cholestadien-24- 57.7 59.2 46.8 49.9ethyl-3-ol (Stigmaserol (8.4%) (8.2%) (7.9%) (8.3%) or poriferasterol) 524-ethylcholest-5-en-  9.64  9.92  9.26 10.2 3-ol (β-Sitosterol or(1.4%) (1.4%) (1.6%) (1.7%) clionasterol) 6 Other sterols 209   221  216   213   Total sterols 685.64 718.82 589.96 601.1 

These results show three striking features. First, ergosterol was foundto be the most abundant of all the sterols, accounting for about 50% ormore of the total sterols. The amount of ergosterol is greater than thatof campesterol, β-sitosterol, and stigmasterol combined. Ergosterol issteroid commonly found in fungus and not commonly found in plants, andits presence particularly in significant amounts serves as a usefulmarker for non-plant oils. Secondly, the oil was found to containbrassicasterol. With the exception of rapeseed oil, brassicasterol isnot commonly found in plant based oils. Thirdly, less than 2%β-sitosterol was found to be present. β-sitosterol is a prominent plantsterol not commonly found in microalgae, and its presence particularlyin significant amounts serves as a useful marker for oils of plantorigin. In summary, Prototheca moriformis strain UTEX1435 has been foundto contain both significant amounts of ergosterol and only trace amountsof β-sitosterol as a percentage of total sterol content. Accordingly,the ratio of ergosterol:β-sitosterol or in combination with the presenceof brassicasterol can be used to distinguish this oil from plant oils.

In some embodiments, the oil content of an oil provided herein contains,as a percentage of total sterols, less than 20%, 15%, 10%, 5%, 4%, 3%,2%, or 1% β-sitosterol. In other embodiments the oil is free fromβ-sitosterol. For any of the oils or cell-oils disclosed in thisapplication, the oil can have the sterol profile of any column of Table5b, above, with a sterol-by-sterol variation of 30%, 20%, 10% or less.

In some embodiments, the oil is free from one or more of β-sitosterol,campesterol, or stigmasterol. In some embodiments the oil is free fromβ-sitosterol, campesterol, and stigmasterol. In some embodiments the oilis free from campesterol. In some embodiments the oil is free fromstigmasterol.

In some embodiments, the oil content of an oil provided hereincomprises, as a percentage of total sterols, less than 20%, 15%, 10%,5%, 4%, 3%, 2%, or 1% 24-ethylcholest-5-en-3-ol. In some embodiments,the 24-ethylcholest-5-en-3-ol is clionasterol. In some embodiments, theoil content of an oil provided herein comprises, as a percentage oftotal sterols, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or 10%clionasterol.

In some embodiments, the oil content of an oil provided herein contains,as a percentage of total sterols, less than 20%, 15%, 10%, 5%, 4%, 3%,2%, or 1% 24-methylcholest-5-en-3-ol. In some embodiments, the24-methylcholest-5-en-3-ol is 22, 23-dihydrobrassicasterol. In someembodiments, the oil content of an oil provided herein comprises, as apercentage of total sterols, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%,9%, or 10% 22,23-dihydrobrassicasterol.

In some embodiments, the oil content of an oil provided herein contains,as a percentage of total sterols, less than 20%, 15%, 10%, 5%, 4%, 3%,2%, or 1% 5, 22-cholestadien-24-ethyl-3-ol. In some embodiments, the 5,22-cholestadien-24-ethyl-3-ol is poriferasterol. In some embodiments,the oil content of an oil provided herein comprises, as a percentage oftotal sterols, at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, or 10%poriferasterol.

In some embodiments, the oil content of an oil provided herein containsergosterol or brassicasterol or a combination of the two. In someembodiments, the oil content contains, as a percentage of total sterols,at least 5%, 10%, 20%, 25%, 35%, 40%, 45%, 50%, 55%, 60%, or 65%ergosterol. In some embodiments, the oil content contains, as apercentage of total sterols, at least 25% ergosterol. In someembodiments, the oil content contains, as a percentage of total sterols,at least 40% ergosterol. In some embodiments, the oil content contains,as a percentage of total sterols, at least 5%, 10%, 20%, 25%, 35%, 40%,45%, 50%, 55%, 60%, or 65% of a combination of ergosterol andbrassicasterol.

In some embodiments, the oil content contains, as a percentage of totalsterols, at least 1%, 2%, 3%, 4% or 5% brassicasterol. In someembodiments, the oil content contains, as a percentage of total sterolsless than 10%, 9%, 8%, 7%, 6%, or 5% brassicasterol.

In some embodiments the ratio of ergosterol to brassicasterol is atleast 5:1, 10:1, 15:1, or 20:1.

In some embodiments, the oil content contains, as a percentage of totalsterols, at least 5%, 10%, 20%, 25%, 35%, 40%, 45%, 50%, 55%, 60%, or65% ergosterol and less than 20%, 15%, 10%, 5%, 4%, 3%, 2%, or 1%β-sitosterol. In some embodiments, the oil content contains, as apercentage of total sterols, at least 25% ergosterol and less than 5%β-sitosterol. In some embodiments, the oil content further comprisesbrassicasterol.

Sterols contain from 27 to 29 carbon atoms (C27 to C29) and are found inall eukaryotes. Animals exclusively make C27 sterols as they lack theability to further modify the C27 sterols to produce C28 and C29sterols. Plants however are able to synthesize C28 and C29 sterols, andC28/C29 plant sterols are often referred to as phytosterols. The sterolprofile of a given plant is high in C29 sterols, and the primary sterolsin plants are typically the C29 sterols b-sitosterol and stigmasterol.In contrast, the sterol profile of non-plant organisms contain greaterpercentages of C27 and C28 sterols. For example the sterols in fungi andin many microalgae are principally C28 sterols. The sterol profile andparticularly the striking predominance of C29 sterols over C28 sterolsin plants has been exploited for determining the proportion of plant andmarine matter in soil samples (Huang, Wen-Yen, Meinschein W. G.,“Sterols as ecological indicators”; Geochimica et Cosmochimia Acta. Vol43. pp 739-745).

In some embodiments the primary sterols in the microalgal oils providedherein are sterols other than b-sitosterol and stigmasterol. In someembodiments of the microalgal oils, C29 sterols make up less than 50%,40%, 30%, 20%, 10%, or 5% by weight of the total sterol content.

In some embodiments the microalgal oils provided herein contain C28sterols in excess of C29 sterols. In some embodiments of the microalgaloils, C28 sterols make up greater than 50%, 60%, 70%, 80%, 90%, or 95%by weight of the total sterol content. In some embodiments the C28sterol is ergosterol. In some embodiments the C28 sterol isbrassicasterol.

XIII. FUELS AND CHEMICALS

The oils discussed above alone or in combination are useful in theproduction of foods, fuels and chemicals (including plastics, foams,films, etc.). The oils, triglycerides, fatty acids from the oils may besubjected to C—H activation, hydroamino methylation,methoxy-carbonation, ozonolysis, enzymatic transformations, epoxidation,methylation, dimerization, thiolation, metathesis, hydro-alkylation,lactonization, or other chemical processes.

The oils can be converted to alkanes (e.g., renewable diesel) or esters(e.g., methyl or ethyl esters for biodisesel produced bytransesterification). The alkanes or esters may be used as fuel, assolvents or lubricants, or as a chemical feedstock. Methods forproduction of renewable diesel and biodiesel are well established in theart. See, for example, WO2011/150411.

In a specific embodiment of the present invention, a high-oleic orhigh-oleic-high stability oil described above is esterified. Forexample, the oils can be transesterified with methanol to an oil that isrich in methyl oleate. As described in Example 49, such formulationshave been found to compare favorably with methyl oleate from soybeanoil.

In another specific example, the oil is converted to C36 diacids orproducts of C36 diacids. Fatty acids produced from the oil can bepolymerized to give a composition rich in C36 dimer acids. In a specificexample, high-oleic oil is split to give a high-oleic fatty acidmaterial which is polymerized to give a composition rich in C36-dimeracids. Optionally , the oil is high oleic high stability oil (e.g.,greater than 60% oleic acid with less than 3% polyunsaturates, greaterthan 70% oleic acid with less than 2% polyunsaturates, or greater than80% oleic acid with less than 1% polyunsaturates). It is believed thatusing a high oleic, high stability, starting material will give loweramounts of cyclic products, which may be desirable in some cases. Afterhydrolyzing the oil, one obtains a high concentration of oleic acid. Inthe process of making dimer acids, a high oleic acid stream will convertto a “cleaner” C36 dimer acid and not produce trimers acids (C54) andother more complex cyclic by-products which are obtained due to presenceof C18:2 and C18:3 acids. For example, the oil can be hydrolyzed tofatty acids and the fatty acids purified and dimerized at 250° C. in thepresence of montmorillonite clay. See SRI Natural Fatty Acid, March2009. A product rich in C36 dimers of oleic acid is recovered.

Further, the C36 dimer acids can be esterified and hydrogenated to givediols. The diols can be polymerized by catalytic dehydration. Polymerscan also be produced by transesterification of dimerdiols with dimethylcarbonate.

For the production of fuel in accordance with the methods of theinvention lipids produced by cells of the invention are harvested, orotherwise collected, by any convenient means. Lipids can be isolated bywhole cell extraction. The cells are first disrupted, and thenintracellular and cell membrane/cell wall-associated lipids as well asextracellular hydrocarbons can be separated from the cell mass, such asby use of centrifugation. Intracellular lipids produced in oleaginouscells are, in some embodiments, extracted after lysing the cells. Onceextracted, the lipids are further refined to produce oils, fuels, oroleochemicals.

Various methods are available for separating lipids from cellularlysates. For example, lipids and lipid derivatives such as fattyaldehydes, fatty alcohols, and hydrocarbons such as alkanes can beextracted with a hydrophobic solvent such as hexane (see Frenz et al.1989, Enzyme Microb. Technol., 11:717). Lipids and lipid derivatives canalso be extracted using liquefaction (see for example Sawayama et al.1999, Biomass and Bioenergy 17:33-39 and Inoue et al. 1993, BiomassBioenergy 6(4):269-274); oil liquefaction (see for example Minowa et al.1995, Fuel 74(12):1735-1738); and supercritical CO₂ extraction (see forexample Mendes et al. 2003, Inorganica Chimica Acta 356:328-334). Miaoand Wu describe a protocol of the recovery of microalgal lipid from aculture of Chlorella protothecoides in which the cells were harvested bycentrifugation, washed with distilled water and dried by freeze drying.The resulting cell powder was pulverized in a mortar and then extractedwith n-hexane. Miao and Wu, Biosource Technology (2006) 97:841-846.

Lipids and lipid derivatives can be recovered by extraction with anorganic solvent. In some cases, the preferred organic solvent is hexane.Typically, the organic solvent is added directly to the lysate withoutprior separation of the lysate components. In one embodiment, the lysategenerated by one or more of the methods described above is contactedwith an organic solvent for a period of time sufficient to allow thelipid and/or hydrocarbon components to form a solution with the organicsolvent. In some cases, the solution can then be further refined torecover specific desired lipid or hydrocarbon components. Hexaneextraction methods are well known in the art.

Lipids produced by cells in vivo, or enzymatically modified in vitro, asdescribed herein can be optionally further processed by conventionalmeans. The processing can include “cracking” to reduce the size, andthus increase the hydrogen:carbon ratio, of hydrocarbon molecules.Catalytic and thermal cracking methods are routinely used in hydrocarbonand triglyceride oil processing. Catalytic methods involve the use of acatalyst, such as a solid acid catalyst. The catalyst can besilica-alumina or a zeolite, which result in the heterolytic, orasymmetric, breakage of a carbon-carbon bond to result in a carbocationand a hydride anion. These reactive intermediates then undergo eitherrearrangement or hydride transfer with another hydrocarbon. Thereactions can thus regenerate the intermediates to result in aself-propagating chain mechanism. Hydrocarbons can also be processed toreduce, optionally to zero, the number of carbon-carbon double, ortriple, bonds therein. Hydrocarbons can also be processed to remove oreliminate a ring or cyclic structure therein. Hydrocarbons can also beprocessed to increase the hydrogen:carbon ratio. This can include theaddition of hydrogen (“hydrogenation”) and/or the “cracking” ofhydrocarbons into smaller hydrocarbons.

Thermal methods involve the use of elevated temperature and pressure toreduce hydrocarbon size. An elevated temperature of about 800° C. andpressure of about 700 kPa can be used. These conditions generate“light,” a term that is sometimes used to refer to hydrogen-richhydrocarbon molecules (as distinguished from photon flux), while alsogenerating, by condensation, heavier hydrocarbon molecules which arerelatively depleted of hydrogen. The methodology provides homolytic, orsymmetrical, breakage and produces alkenes, which may be optionallyenzymatically saturated as described above.

Catalytic and thermal methods are standard in plants for hydrocarbonprocessing and oil refining. Thus hydrocarbons produced by cells asdescribed herein can be collected and processed or refined viaconventional means. See Hillen et al. (Biotechnology and Bioengineering,Vol. XXIV:193-205 (1982)) for a report on hydrocracking ofmicroalgae-produced hydrocarbons. In alternative embodiments, thefraction is treated with another catalyst, such as an organic compound,heat, and/or an inorganic compound. For processing of lipids intobiodiesel, a transesterification process is used as described below inthis Section.

Hydrocarbons produced via methods of the present invention are useful ina variety of industrial applications. For example, the production oflinear alkylbenzene sulfonate (LAS), an anionic surfactant used innearly all types of detergents and cleaning preparations, utilizeshydrocarbons generally comprising a chain of 10-14 carbon atoms. See,for example, U.S. Pat. Nos. 6,946,430; 5,506,201; 6,692,730; 6,268,517;6,020,509; 6,140,302; 5,080,848; and 5,567,359. Surfactants, such asLAS, can be used in the manufacture of personal care compositions anddetergents, such as those described in U.S. Pat. Nos. 5,942,479;6,086,903; 5,833,999; 6,468,955; and 6,407,044.

Increasing interest is directed to the use of hydrocarbon components ofbiological origin in fuels, such as biodiesel, renewable diesel, and jetfuel, since renewable biological starting materials that may replacestarting materials derived from fossil fuels are available, and the usethereof is desirable. There is an urgent need for methods for producinghydrocarbon components from biological materials. The present inventionfulfills this need by providing methods for production of biodiesel,renewable diesel, and jet fuel using the lipids generated by the methodsdescribed herein as a biological material to produce biodiesel,renewable diesel, and jet fuel.

Traditional diesel fuels are petroleum distillates rich in paraffinichydrocarbons. They have boiling ranges as broad as 370° to 780° F.,which are suitable for combustion in a compression ignition engine, suchas a diesel engine vehicle. The American Society of Testing andMaterials (ASTM) establishes the grade of diesel according to theboiling range, along with allowable ranges of other fuel properties,such as cetane number, cloud point, flash point, viscosity, anilinepoint, sulfur content, water content, ash content, copper stripcorrosion, and carbon residue. Technically, any hydrocarbon distillatematerial derived from biomass or otherwise that meets the appropriateASTM specification can be defined as diesel fuel (ASTM D975), jet fuel(ASTM D1655), or as biodiesel if it is a fatty acid methyl ester (ASTMD6751).

After extraction, lipid and/or hydrocarbon components recovered from themicrobial biomass described herein can be subjected to chemicaltreatment to manufacture a fuel for use in diesel vehicles and jetengines.

Biodiesel is a liquid which varies in color—between golden and darkbrown—depending on the production feedstock. It is practicallyimmiscible with water, has a high boiling point and low vapor pressure.Biodiesel refers to a diesel-equivalent processed fuel for use indiesel-engine vehicles. Biodiesel is biodegradable and non-toxic. Anadditional benefit of biodiesel over conventional diesel fuel is lowerengine wear. Typically, biodiesel comprises C14-C18 alkyl esters.Various processes convert biomass or a lipid produced and isolated asdescribed herein to diesel fuels. A preferred method to producebiodiesel is by transesterification of a lipid as described herein. Apreferred alkyl ester for use as biodiesel is a methyl ester or ethylester.

Biodiesel produced by a method described herein can be used alone orblended with conventional diesel fuel at any concentration in mostmodern diesel-engine vehicles. When blended with conventional dieselfuel (petroleum diesel), biodiesel may be present from about 0.1% toabout 99.9%. Much of the world uses a system known as the “B” factor tostate the amount of biodiesel in any fuel mix. For example, fuelcontaining 20% biodiesel is labeled B20. Pure biodiesel is referred toas B100.

Biodiesel can be produced by transesterification of triglyceridescontained in oil-rich biomass. Thus, in another aspect of the presentinvention a method for producing biodiesel is provided. In a preferredembodiment, the method for producing biodiesel comprises the steps of(a) cultivating a lipid-containing microorganism using methods disclosedherein (b) lysing a lipid-containing microorganism to produce a lysate,(c) isolating lipid from the lysed microorganism, and (d)transesterifying the lipid composition, whereby biodiesel is produced.Methods for growth of a microorganism, lysing a microorganism to producea lysate, treating the lysate in a medium comprising an organic solventto form a heterogeneous mixture and separating the treated lysate into alipid composition have been described above and can also be used in themethod of producing biodiesel. The lipid profile of the biodiesel isusually highly similar to the lipid profile of the feedstock oil.

Lipid compositions can be subjected to transesterification to yieldlong-chain fatty acid esters useful as biodiesel. Preferredtransesterification reactions are outlined below and include basecatalyzed transesterification and transesterification using recombinantlipases. In a base-catalyzed transesterification process, thetriacylglycerides are reacted with an alcohol, such as methanol orethanol, in the presence of an alkaline catalyst, typically potassiumhydroxide. This reaction forms methyl or ethyl esters and glycerin(glycerol) as a byproduct.

Transesterification has also been carried out, as discussed above, usingan enzyme, such as a lipase instead of a base. Lipase-catalyzedtransesterification can be carried out, for example, at a temperaturebetween the room temperature and 80° C., and a mole ratio of the TAG tothe lower alcohol of greater than 1:1, preferably about 3:1. Lipasessuitable for use in transesterification include, but are not limited to,those listed in Table 9. Other examples of lipases useful fortransesterification are found in, e.g., U.S. Pat. Nos. 4,798,793;4,940,845 5,156,963; 5,342,768; 5,776,741 and WO89/01032. Such lipasesinclude, but are not limited to, lipases produced by microorganisms ofRhizopus, Aspergillus, Candida, Mucor, Pseudomonas, Rhizomucor, Candida,and Humicola and pancreas lipase.

Subsequent processes may also be used if the biodiesel will be used inparticularly cold temperatures. Such processes include winterization andfractionation. Both processes are designed to improve the cold flow andwinter performance of the fuel by lowering the cloud point (thetemperature at which the biodiesel starts to crystallize). There areseveral approaches to winterizing biodiesel. One approach is to blendthe biodiesel with petroleum diesel. Another approach is to useadditives that can lower the cloud point of biodiesel. Another approachis to remove saturated methyl esters indiscriminately by mixing inadditives and allowing for the crystallization of saturates and thenfiltering out the crystals. Fractionation selectively separates methylesters into individual components or fractions, allowing for the removalor inclusion of specific methyl esters. Fractionation methods includeurea fractionation, solvent fractionation and thermal distillation.

Another valuable fuel provided by the methods of the present inventionis renewable diesel, which comprises alkanes, such as C10:0, C12:0,C14:0, C16:0 and C18:0 and thus, are distinguishable from biodiesel.High quality renewable diesel conforms to the ASTM D975 standard. Thelipids produced by the methods of the present invention can serve asfeedstock to produce renewable diesel. Thus, in another aspect of thepresent invention, a method for producing renewable diesel is provided.Renewable diesel can be produced by at least three processes:hydrothermal processing (hydrotreating); hydroprocessing; and indirectliquefaction. These processes yield non-ester distillates. During theseprocesses, triacylglycerides produced and isolated as described herein,are converted to alkanes.

In one embodiment, the method for producing renewable diesel comprises(a) cultivating a lipid-containing microorganism using methods disclosedherein (b) lysing the microorganism to produce a lysate, (c) isolatinglipid from the lysed microorganism, and (d) deoxygenating andhydrotreating the lipid to produce an alkane, whereby renewable dieselis produced. Lipids suitable for manufacturing renewable diesel can beobtained via extraction from microbial biomass using an organic solventsuch as hexane, or via other methods, such as those described in U.S.Pat. No. 5,928,696. Some suitable methods may include mechanicalpressing and centrifuging.

In some methods, the microbial lipid is first cracked in conjunctionwith hydrotreating to reduce carbon chain length and saturate doublebonds, respectively. The material is then isomerized, also inconjunction with hydrotreating. The naptha fraction can then be removedthrough distillation, followed by additional distillation to vaporizeand distill components desired in the diesel fuel to meet an ASTM D975standard while leaving components that are heavier than desired formeeting the D975 standard. Hydrotreating, hydrocracking, deoxygenationand isomerization methods of chemically modifying oils, includingtriglyceride oils, are well known in the art. See for example Europeanpatent applications EP1741768 (A1); EP1741767 (A1); EP1682466 (A1);EP1640437 (A1); EP1681337 (A1); EP1795576 (A1); and U.S. Pat. Nos.7,238,277; 6,630,066; 6,596,155; 6,977,322; 7,041,866; 6,217,746;5,885,440; 6,881,873.

In one embodiment of the method for producing renewable diesel, treatingthe lipid to produce an alkane is performed by hydrotreating of thelipid composition. In hydrothermal processing, typically, biomass isreacted in water at an elevated temperature and pressure to form oilsand residual solids. Conversion temperatures are typically 300° to 660°F., with pressure sufficient to keep the water primarily as a liquid,100 to 170 standard atmosphere (atm). Reaction times are on the order of15 to 30 minutes. After the reaction is completed, the organics areseparated from the water. Thereby a distillate suitable for diesel isproduced.

In some methods of making renewable diesel, the first step of treating atriglyceride is hydroprocessing to saturate double bonds, followed bydeoxygenation at elevated temperature in the presence of hydrogen and acatalyst. In some methods, hydrogenation and deoxygenation occur in thesame reaction. In other methods deoxygenation occurs beforehydrogenation. Isomerization is then optionally performed, also in thepresence of hydrogen and a catalyst. Naphtha components are preferablyremoved through distillation. For examples, see U.S. Pat. No. 5,475,160(hydrogenation of triglycerides); U.S. Pat. No. 5,091,116(deoxygenation, hydrogenation and gas removal); U.S. Pat. No. 6,391,815(hydrogenation); and U.S. Pat. No. 5,888,947 (isomerization).

One suitable method for the hydrogenation of triglycerides includespreparing an aqueous solution of copper, zinc, magnesium and lanthanumsalts and another solution of alkali metal or preferably, ammoniumcarbonate. The two solutions may be heated to a temperature of about 20°C. to about 85° C. and metered together into a precipitation containerat rates such that the pH in the precipitation container is maintainedbetween 5.5 and 7.5 in order to form a catalyst. Additional water may beused either initially in the precipitation container or addedconcurrently with the salt solution and precipitation solution. Theresulting precipitate may then be thoroughly washed, dried, calcined atabout 300° C. and activated in hydrogen at temperatures ranging fromabout 100° C. to about 400° C. One or more triglycerides may then becontacted and reacted with hydrogen in the presence of theabove-described catalyst in a reactor. The reactor may be a trickle bedreactor, fixed bed gas-solid reactor, packed bubble column reactor,continuously stirred tank reactor, a slurry phase reactor, or any othersuitable reactor type known in the art. The process may be carried outeither batchwise or in continuous fashion. Reaction temperatures aretypically in the range of from about 170° C. to about 250° C. whilereaction pressures are typically in the range of from about 300 psig toabout 2000 psig. Moreover, the molar ratio of hydrogen to triglyceridein the process of the present invention is typically in the range offrom about 20:1 to about 700:1. The process is typically carried out ata weight hourly space velocity (WHSV) in the range of from about 0.1hr⁻¹ to about 5 hr⁻¹. One skilled in the art will recognize that thetime period required for reaction will vary according to the temperatureused, the molar ratio of hydrogen to triglyceride, and the partialpressure of hydrogen. The products produced by the such hydrogenationprocesses include fatty alcohols, glycerol, traces of paraffins andunreacted triglycerides. These products are typically separated byconventional means such as, for example, distillation, extraction,filtration, crystallization, and the like.

Petroleum refiners use hydroprocessing to remove impurities by treatingfeeds with hydrogen. Hydroprocessing conversion temperatures aretypically 300° to 700° F. Pressures are typically 40 to 100 atm. Thereaction times are typically on the order of 10 to 60 minutes. Solidcatalysts are employed to increase certain reaction rates, improveselectivity for certain products, and optimize hydrogen consumption.

Suitable methods for the deoxygenation of an oil includes heating an oilto a temperature in the range of from about 350° F. to about 550° F. andcontinuously contacting the heated oil with nitrogen under at leastpressure ranging from about atmospheric to above for at least about 5minutes.

Suitable methods for isomerization include using alkali isomerizationand other oil isomerization known in the art.

Hydrotreating and hydroprocessing ultimately lead to a reduction in themolecular weight of the triglyceride feed. The triglyceride molecule isreduced to four hydrocarbon molecules under hydroprocessing conditions:a propane molecule and three heavier hydrocarbon molecules, typically inthe C8 to C18 range.

Thus, in one embodiment, the product of one or more chemical reaction(s)performed on lipid compositions of the invention is an alkane mixturethat comprises ASTM D975 renewable diesel. Production of hydrocarbons bymicroorganisms is reviewed by Metzger et al. Appl Microbiol Biotechnol(2005) 66: 486-496 and A Look Back at the U.S. Department of Energy'sAquatic Species Program: Biodiesel from Algae, NREL/TP-580-24190, JohnSheehan, Terri Dunahay, John Benemann and Paul Roessler (1998).

The distillation properties of a diesel fuel is described in terms ofT10-T90 (temperature at 10% and 90%, respectively, volume distilled).The T10-T90 of the material produced in Example 13 was 57.9° C. Methodsof hydrotreating, isomerization, and other covalent modification of oilsdisclosed herein, as well as methods of distillation and fractionation(such as cold filtration) disclosed herein, can be employed to generaterenewable diesel compositions with other T10-T90 ranges, such as 20, 25,30, 35, 40, 45, 50, 60 and 65° C. using triglyceride oils producedaccording to the methods disclosed herein.

Methods of hydrotreating, isomerization, and other covalent modificationof oils disclosed herein, as well as methods of distillation andfractionation (such as cold filtration) disclosed herein, can beemployed to generate renewable diesel compositions with other T10values, such as T10 between 180 and 295, between 190 and 270, between210 and 250, between 225 and 245, and at least 290.

Methods of hydrotreating, isomerization, and other covalent modificationof oils disclosed herein, as well as methods of distillation andfractionation (such as cold filtration) disclosed herein can be employedto generate renewable diesel compositions with certain T90 values, suchas T90 between 280 and 380, between 290 and 360, between 300 and 350,between 310 and 340, and at least 290.

The FBP of the material produced in Example 13 was 300° C. Methods ofhydrotreating, isomerization, and other covalent modification of oilsdisclosed herein, as well as methods of distillation and fractionation(such as cold filtration) disclosed herein, can be employed to generaterenewable diesel compositions with other FBP values, such as FBP between290 and 400, between 300 and 385, between 310 and 370, between 315 and360, and at least 300.

Other oils provided by the methods and compositions of the invention canbe subjected to combinations of hydrotreating, isomerization, and othercovalent modification including oils with lipid profiles including (a)at least 1%-5%, preferably at least 4%, C8-C14; (b) at least 0.25%-1%,preferably at least 0.3%, C8; (c) at least 1%-5%, preferably at least2%, C10; (d) at least 1%-5%, preferably at least 2%, C12; and (3) atleast 20%-40%, preferably at least 30% C8-C14.

A traditional ultra-low sulfur diesel can be produced from any form ofbiomass by a two-step process. First, the biomass is converted to asyngas, a gaseous mixture rich in hydrogen and carbon monoxide. Then,the syngas is catalytically converted to liquids. Typically, theproduction of liquids is accomplished using Fischer-Tropsch (FT)synthesis. This technology applies to coal, natural gas, and heavy oils.Thus, in yet another preferred embodiment of the method for producingrenewable diesel, treating the lipid composition to produce an alkane isperformed by indirect liquefaction of the lipid composition.

The present invention also provides methods to produce jet fuel. Jetfuel is clear to straw colored. The most common fuel is anunleaded/paraffin oil-based fuel classified as Aeroplane A-1, which isproduced to an internationally standardized set of specifications. Jetfuel is a mixture of a large number of different hydrocarbons, possiblyas many as a thousand or more. The range of their sizes (molecularweights or carbon numbers) is restricted by the requirements for theproduct, for example, freezing point or smoke point. Kerosene-typeAeroplane fuel (including Jet A and Jet A-1) has a carbon numberdistribution between about 8 and 16 carbon numbers. Wide-cut ornaphtha-type Aeroplane fuel (including Jet B) typically has a carbonnumber distribution between about 5 and 15 carbons.

In one embodiment of the invention, a jet fuel is produced by blendingalgal fuels with existing jet fuel. The lipids produced by the methodsof the present invention can serve as feedstock to produce jet fuel.Thus, in another aspect of the present invention, a method for producingjet fuel is provided. Herewith two methods for producing jet fuel fromthe lipids produced by the methods of the present invention areprovided: fluid catalytic cracking (FCC); and hydrodeoxygenation (HDO).

Fluid Catalytic Cracking (FCC) is one method which is used to produceolefins, especially propylene from heavy crude fractions. The lipidsproduced by the method of the present invention can be converted toolefins. The process involves flowing the lipids produced through an FCCzone and collecting a product stream comprised of olefins, which isuseful as a jet fuel. The lipids produced are contacted with a crackingcatalyst at cracking conditions to provide a product stream comprisingolefins and hydrocarbons useful as jet fuel.

In one embodiment, the method for producing jet fuel comprises (a)cultivating a lipid-containing microorganism using methods disclosedherein, (b) lysing the lipid-containing microorganism to produce alysate, (c) isolating lipid from the lysate, and (d) treating the lipidcomposition, whereby jet fuel is produced. In one embodiment of themethod for producing a jet fuel, the lipid composition can be flowedthrough a fluid catalytic cracking zone, which, in one embodiment, maycomprise contacting the lipid composition with a cracking catalyst atcracking conditions to provide a product stream comprising C₂-C₅olefins.

In certain embodiments of this method, it may be desirable to remove anycontaminants that may be present in the lipid composition. Thus, priorto flowing the lipid composition through a fluid catalytic crackingzone, the lipid composition is pretreated. Pretreatment may involvecontacting the lipid composition with an ion-exchange resin. The ionexchange resin is an acidic ion exchange resin, such as Amberlyst™-15and can be used as a bed in a reactor through which the lipidcomposition is flowed, either upflow or downflow. Other pretreatmentsmay include mild acid washes by contacting the lipid composition with anacid, such as sulfuric, acetic, nitric, or hydrochloric acid. Contactingis done with a dilute acid solution usually at ambient temperature andatmospheric pressure.

The lipid composition, optionally pretreated, is flowed to an FCC zonewhere the hydrocarbonaceous components are cracked to olefins. Catalyticcracking is accomplished by contacting the lipid composition in areaction zone with a catalyst composed of finely divided particulatematerial. The reaction is catalytic cracking, as opposed tohydrocracking, and is carried out in the absence of added hydrogen orthe consumption of hydrogen. As the cracking reaction proceeds,substantial amounts of coke are deposited on the catalyst. The catalystis regenerated at high temperatures by burning coke from the catalyst ina regeneration zone. Coke-containing catalyst, referred to herein as“coked catalyst”, is continually transported from the reaction zone tothe regeneration zone to be regenerated and replaced by essentiallycoke-free regenerated catalyst from the regeneration zone. Fluidizationof the catalyst particles by various gaseous streams allows thetransport of catalyst between the reaction zone and regeneration zone.Methods for cracking hydrocarbons, such as those of the lipidcomposition described herein, in a fluidized stream of catalyst,transporting catalyst between reaction and regeneration zones, andcombusting coke in the regenerator are well known by those skilled inthe art of FCC processes. Exemplary FCC applications and catalystsuseful for cracking the lipid composition to produce C₂-C₅ olefins aredescribed in U.S. Pat. Nos. 6,538,169, 7,288,685, which are incorporatedin their entirety by reference.

Suitable FCC catalysts generally comprise at least two components thatmay or may not be on the same matrix. In some embodiments, both twocomponents may be circulated throughout the entire reaction vessel. Thefirst component generally includes any of the well-known catalysts thatare used in the art of fluidized catalytic cracking, such as an activeamorphous clay-type catalyst and/or a high activity, crystallinemolecular sieve. Molecular sieve catalysts may be preferred overamorphous catalysts because of their much-improved selectivity todesired products. In some preferred embodiments, zeolites may be used asthe molecular sieve in the FCC processes. Preferably, the first catalystcomponent comprises a large pore zeolite, such as a Y-type zeolite, anactive alumina material, a binder material, comprising either silica oralumina and an inert filler such as kaolin.

In one embodiment, cracking the lipid composition of the presentinvention, takes place in the riser section or, alternatively, the liftsection, of the FCC zone. The lipid composition is introduced into theriser by a nozzle resulting in the rapid vaporization of the lipidcomposition. Before contacting the catalyst, the lipid composition willordinarily have a temperature of about 149° C. to about 316° C. (300° F.to 600° F.). The catalyst is flowed from a blending vessel to the riserwhere it contacts the lipid composition for a time of abort 2 seconds orless.

The blended catalyst and reacted lipid composition vapors are thendischarged from the top of the riser through an outlet and separatedinto a cracked product vapor stream including olefins and a collectionof catalyst particles covered with substantial quantities of coke andgenerally referred to as “coked catalyst.” In an effort to minimize thecontact time of the lipid composition and the catalyst which may promotefurther conversion of desired products to undesirable other products,any arrangement of separators such as a swirl arm arrangement can beused to remove coked catalyst from the product stream quickly. Theseparator, e.g. swirl arm separator, is located in an upper portion of achamber with a stripping zone situated in the lower portion of thechamber. Catalyst separated by the swirl arm arrangement drops down intothe stripping zone. The cracked product vapor stream comprising crackedhydrocarbons including light olefins and some catalyst exit the chambervia a conduit which is in communication with cyclones. The cyclonesremove remaining catalyst particles from the product vapor stream toreduce particle concentrations to very low levels. The product vaporstream then exits the top of the separating vessel. Catalyst separatedby the cyclones is returned to the separating vessel and then to thestripping zone. The stripping zone removes adsorbed hydrocarbons fromthe surface of the catalyst by counter-current contact with steam.

Low hydrocarbon partial pressure operates to favor the production oflight olefins. Accordingly, the riser pressure is set at about 172 to241 kPa (25 to 35 psia) with a hydrocarbon partial pressure of about 35to 172 kPa (5 to 25 psia), with a preferred hydrocarbon partial pressureof about 69 to 138 kPa (10 to 20 psia). This relatively low partialpressure for hydrocarbon is achieved by using steam as a diluent to theextent that the diluent is 10 to 55 wt-% of lipid composition andpreferably about 15 wt-% of lipid composition. Other diluents such asdry gas can be used to reach equivalent hydrocarbon partial pressures.

The temperature of the cracked stream at the riser outlet will be about510° C. to 621° C. (950° F. to 1150° F.). However, riser outlettemperatures above 566° C. (1050° F.) make more dry gas and moreolefins. Whereas, riser outlet temperatures below 566° C. (1050° F.)make less ethylene and propylene. Accordingly, it is preferred to runthe FCC process at a preferred temperature of about 566° C. to about630° C., preferred pressure of about 138 kPa to about 240 kPa (20 to 35psia). Another condition for the process is the catalyst to lipidcomposition ratio which can vary from about 5 to about 20 and preferablyfrom about 10 to about 15.

In one embodiment of the method for producing a jet fuel, the lipidcomposition is introduced into the lift section of an FCC reactor. Thetemperature in the lift section will be very hot and range from about700° C. (1292° F.) to about 760° C. (1400° F.) with a catalyst to lipidcomposition ratio of about 100 to about 150. It is anticipated thatintroducing the lipid composition into the lift section will produceconsiderable amounts of propylene and ethylene.

In another embodiment of the method for producing a jet fuel using thelipid composition or the lipids produced as described herein, thestructure of the lipid composition or the lipids is broken by a processreferred to as hydrodeoxygenation (HDO). HDO means removal of oxygen bymeans of hydrogen, that is, oxygen is removed while breaking thestructure of the material. Olefinic double bonds are hydrogenated andany sulfur and nitrogen compounds are removed. Sulfur removal is calledhydrodesulphurization (HDS). Pretreatment and purity of the rawmaterials (lipid composition or the lipids) contribute to the servicelife of the catalyst.

Generally in the HDO/HDS step, hydrogen is mixed with the feed stock(lipid composition or the lipids) and then the mixture is passed througha catalyst bed as a co-current flow, either as a single phase or a twophase feed stock. After the HDO/MDS step, the product fraction isseparated and passed to a separate isomerization reactor. Anisomerization reactor for biological starting material is described inthe literature (FI 100 248) as a co-current reactor.

The process for producing a fuel by hydrogenating a hydrocarbon feed,e.g., the lipid composition or the lipids herein, can also be performedby passing the lipid composition or the lipids as a co-current flow withhydrogen gas through a first hydrogenation zone, and thereafter thehydrocarbon effluent is further hydrogenated in a second hydrogenationzone by passing hydrogen gas to the second hydrogenation zone as acounter-current flow relative to the hydrocarbon effluent. Exemplary HDOapplications and catalysts useful for cracking the lipid composition toproduce C₂-C₅ olefins are described in U.S. Pat. No. 7,232,935, which isincorporated in its entirety by reference.

Typically, in the hydrodeoxygenation step, the structure of thebiological component, such as the lipid composition or lipids herein, isdecomposed, oxygen, nitrogen, phosphorus and sulfur compounds, and lighthydrocarbons as gas are removed, and the olefinic bonds arehydrogenated. In the second step of the process, i.e. in the so-calledisomerization step, isomerization is carried out for branching thehydrocarbon chain and improving the performance of the paraffin at lowtemperatures.

In the first step, i.e. HDO step, of the cracking process, hydrogen gasand the lipid composition or lipids herein which are to be hydrogenatedare passed to a HDO catalyst bed system either as co-current orcounter-current flows, said catalyst bed system comprising one or morecatalyst bed(s), preferably 1-3 catalyst beds. The HDO step is typicallyoperated in a co-current manner. In case of a HDO catalyst bed systemcomprising two or more catalyst beds, one or more of the beds may beoperated using the counter-current flow principle. In the HDO step, thepressure varies between 20 and 150 bar, preferably between 50 and 100bar, and the temperature varies between 200 and 500° C., preferably inthe range of 300-400° C. In the HDO step, known hydrogenation catalystscontaining metals from Group VII and/or VIB of the Periodic System maybe used. Preferably, the hydrogenation catalysts are supported Pd, Pt,Ni, NiMo or a CoMo catalysts, the support being alumina and/or silica.Typically, NiMo/Al₂O₃ and CoMo/Al₂O₃ catalysts are used.

Prior to the HDO step, the lipid composition or lipids herein mayoptionally be treated by prehydrogenation under milder conditions thusavoiding side reactions of the double bonds. Such prehydrogenation iscarried out in the presence of a prehydrogenation catalyst attemperatures of 50-400° C. and at hydrogen pressures of 1-200 bar,preferably at a temperature between 150 and 250° C. and at a hydrogenpressure between 10 and 100 bar. The catalyst may contain metals fromGroup VIII and/or VIB of the Periodic System. Preferably, theprehydrogenation catalyst is a supported Pd, Pt, Ni, NiMo or a CoMocatalyst, the support being alumina and/or silica.

A gaseous stream from the HDO step containing hydrogen is cooled andthen carbon monoxide, carbon dioxide, nitrogen, phosphorus and sulfurcompounds, gaseous light hydrocarbons and other impurities are removedtherefrom. After compressing, the purified hydrogen or recycled hydrogenis returned back to the first catalyst bed and/or between the catalystbeds to make up for the withdrawn gas stream. Water is removed from thecondensed liquid. The liquid is passed to the first catalyst bed orbetween the catalyst beds.

After the HDO step, the product is subjected to an isomerization step.It is substantial for the process that the impurities are removed ascompletely as possible before the hydrocarbons are contacted with theisomerization catalyst. The isomerization step comprises an optionalstripping step, wherein the reaction product from the HDO step may bepurified by stripping with water vapor or a suitable gas such as lighthydrocarbon, nitrogen or hydrogen. The optional stripping step iscarried out in counter-current manner in a unit upstream of theisomerization catalyst, wherein the gas and liquid are contacted witheach other, or before the actual isomerization reactor in a separatestripping unit utilizing counter-current principle.

After the stripping step the hydrogen gas and the hydrogenated lipidcomposition or lipids herein, and optionally an n-paraffin mixture, arepassed to a reactive isomerization unit comprising one or severalcatalyst bed(s). The catalyst beds of the isomerization step may operateeither in co-current or counter-current manner.

It is important for the process that the counter-current flow principleis applied in the isomerization step. In the isomerization step this isdone by carrying out either the optional stripping step or theisomerization reaction step or both in counter-current manner. In theisomerization step, the pressure varies in the range of 20-150 bar,preferably in the range of 20-100 bar, the temperature being between 200and 500° C., preferably between 300 and 400° C. In the isomerizationstep, isomerization catalysts known in the art may be used. Suitableisomerization catalysts contain molecular sieve and/or a metal fromGroup VII and/or a carrier. Preferably, the isomerization catalystcontains SAPO-11 or SAPO41 or ZSM-22 or ZSM-23 or ferrierite and Pt, Pdor Ni and Al₂O₃ or SiO₂. Typical isomerization catalysts are, forexample, Pt/SAPO-11/Al₂O₃, Pt/ZSM-22/Al₂O₃, Pt/ZSM-23/Al₂O₃ andPt/SAPO-11/SiO₂. The isomerization step and the HDO step may be carriedout in the same pressure vessel or in separate pressure vessels.Optional prehydrogenation may be carried out in a separate pressurevessel or in the same pressure vessel as the HDO and isomerizationsteps.

Thus, in one embodiment, the product of one or more chemical reactionsis an alkane mixture that comprises HRJ-5. In another embodiment, theproduct of the one or more chemical reactions is an alkane mixture thatcomprises ASTM D1655 jet fuel. In some embodiments, the compositionconforming to the specification of ASTM 1655 jet fuel has a sulfurcontent that is less than 10 ppm. In other embodiments, the compositionconforming to the specification of ASTM 1655 jet fuel has a T10 value ofthe distillation curve of less than 205° C. In another embodiment, thecomposition conforming to the specification of ASTM 1655 jet fuel has afinal boiling point (FBP) of less than 300° C. In another embodiment,the composition conforming to the specification of ASTM 1655 jet fuelhas a flash point of at least 38° C. In another embodiment, thecomposition conforming to the specification of ASTM 1655 jet fuel has adensity between 775K/M³ and 840K/M³. In yet another embodiment, thecomposition conforming to the specification of ASTM 1655 jet fuel has afreezing point that is below −47° C. In another embodiment, thecomposition conforming to the specification of ASTM 1655 jet fuel has anet Heat of Combustion that is at least 42.8 MJ/K. In anotherembodiment, the composition conforming to the specification of ASTM 1655jet fuel has a hydrogen content that is at least 13.4 mass %. In anotherembodiment, the composition conforming to the specification of ASTM 1655jet fuel has a thermal stability, as tested by quantitative gravimetricJFTOT at 260° C., which is below 3 mm of Hg. In another embodiment, thecomposition conforming to the specification of ASTM 1655 jet fuel has anexistent gum that is below 7 mg/dl.

Thus, the present invention discloses a variety of methods in whichchemical modification of microalgal lipid is undertaken to yieldproducts useful in a variety of industrial and other applications.Examples of processes for modifying oil produced by the methodsdisclosed herein include, but are not limited to, hydrolysis of the oil,hydroprocessing of the oil, and esterification of the oil. Otherchemical modification of microalgal lipid include, without limitation,epoxidation, oxidation, hydrolysis, sulfations, sulfonation,ethoxylation, propoxylation, amidation, and saponification. Themodification of the microalgal oil produces basic oleochemicals that canbe further modified into selected derivative oleochemicals for a desiredfunction. In a manner similar to that described above with reference tofuel producing processes, these chemical modifications can also beperformed on oils generated from the microbial cultures describedherein. Examples of basic oleochemicals include, but are not limited to,soaps, fatty acids, fatty esters, fatty alcohols, fatty nitrogencompounds including fatty amides, fatty acid methyl esters, andglycerol. Examples of derivative oleochemicals include, but are notlimited to, fatty nitriles, esters, dimer acids, quats (includingbetaines), surfactants, fatty alkanolamides, fatty alcohol sulfates,resins, emulsifiers, fatty alcohols, olefins, drilling muds, polyols,polyurethanes, polyacrylates, rubber, candles, cosmetics, metallicsoaps, soaps, alpha-sulphonated methyl esters, fatty alcohol sulfates,fatty alcohol ethoxylates, fatty alcohol ether sulfates, imidazolines,surfactants, detergents, esters, quats (including betaines), ozonolysisproducts, fatty amines, fatty alkanolamides, ethoxysulfates,monoglycerides, diglycerides, triglycerides (including medium chaintriglycerides), lubricants, hydraulic fluids, greases, dielectricfluids, mold release agents, metal working fluids, heat transfer fluids,other functional fluids, industrial chemicals (e.g., cleaners, textileprocessing aids, plasticizers, stabilizers, additives), surfacecoatings, paints and lacquers, electrical wiring insulation, and higheralkanes. Other derivatives include fatty amidoamines, amidoaminecarboxylates, amidoamine oxides, amidoamine oxide carboxylates,amidoamine esters, ethanolamine amides, sulfonates, amidoaminesulfonates, diamidoamine dioxides, sulfonated alkyl ester alkoxylates,betaines, quarternized diamidoamine betaines, and sulfobetaines.

Hydrolysis of the fatty acid constituents from the glycerolipidsproduced by the methods of the invention yields free fatty acids thatcan be derivatized to produce other useful chemicals. Hydrolysis occursin the presence of water and a catalyst which may be either an acid or abase. The liberated free fatty acids can be derivatized to yield avariety of products, as reported in the following: U.S. Pat. No.5,304,664 (Highly sulfated fatty acids); U.S. Pat. No. 7,262,158(Cleansing compositions); U.S. Pat. No. 7,115,173 (Fabric softenercompositions); U.S. Pat. No. 6,342,208 (Emulsions for treating skin);U.S. Pat. No. 7,264,886 (Water repellent compositions); U.S. Pat. No.6,924,333 (Paint additives); U.S. Pat. No. 6,596,768 (Lipid-enrichedruminant feedstock); and U.S. Pat. No. 6,380,410 (Surfactants fordetergents and cleaners).

In some methods, the first step of chemical modification may behydroprocessing to saturate double bonds, followed by deoxygenation atelevated temperature in the presence of hydrogen and a catalyst. Inother methods, hydrogenation and deoxygenation may occur in the samereaction. In still other methods deoxygenation occurs beforehydrogenation. Isomerization may then be optionally performed, also inthe presence of hydrogen and a catalyst. Finally, gases and naphthacomponents can be removed if desired. For example, see U.S. Pat. No.5,475,160 (hydrogenation of triglycerides); U.S. Pat. No. 5,091,116(deoxygenation, hydrogenation and gas removal); U.S. Pat. No. 6,391,815(hydrogenation); and U.S. Pat. No. 5,888,947 (isomerization).

In some embodiments of the invention, the triglyceride oils arepartially or completely deoxygenated. The deoxygenation reactions formdesired products, including, but not limited to, fatty acids, fattyalcohols, polyols, ketones, and aldehydes. In general, without beinglimited by any particular theory, the deoxygenation reactions involve acombination of various different reaction pathways, including withoutlimitation: hydrogenolysis, hydrogenation, consecutivehydrogenation-hydrogenolysis, consecutive hydrogenolysis-hydrogenation,and combined hydrogenation-hydrogenolysis reactions, resulting in atleast the partial removal of oxygen from the fatty acid or fatty acidester to produce reaction products, such as fatty alcohols, that can beeasily converted to the desired chemicals by further processing. Forexample, in one embodiment, a fatty alcohol may be converted to olefinsthrough FCC reaction or to higher alkanes through a condensationreaction.

One such chemical modification is hydrogenation, which is the additionof hydrogen to double bonds in the fatty acid constituents ofglycerolipids or of free fatty acids. The hydrogenation process permitsthe transformation of liquid oils into semi-solid or solid fats, whichmay be more suitable for specific applications.

Hydrogenation of oil produced by the methods described herein can beperformed in conjunction with one or more of the methods and/ormaterials provided herein, as reported in the following: U.S. Pat. No.7,288,278 (Food additives or medicaments); U.S. Pat. No. 5,346,724(Lubrication products); U.S. Pat. No. 5,475,160 (Fatty alcohols); U.S.Pat. No. 5,091,116 (Edible oils); U.S. Pat. No. 6,808,737 (Structuralfats for margarine and spreads); U.S. Pat. No. 5,298,637(Reduced-calorie fat substitutes); U.S. Pat. No. 6,391,815(Hydrogenation catalyst and sulfur adsorbent); U.S. Pat. No. 5,233,099and U.S. Pat. No. 5,233,100 (Fatty alcohols); U.S. Pat. No. 4,584,139(Hydrogenation catalysts); U.S. Pat. No. 6,057,375 (Foam suppressingagents); and U.S. Pat. No. 7,118,773 (Edible emulsion spreads).

One skilled in the art will recognize that various processes may be usedto hydrogenate carbohydrates. One suitable method includes contactingthe carbohydrate with hydrogen or hydrogen mixed with a suitable gas anda catalyst under conditions sufficient in a hydrogenation reactor toform a hydrogenated product. The hydrogenation catalyst generally caninclude Cu, Re, Ni, Fe, Co, Ru, Pd, Rh, Pt, Os, Ir, and alloys or anycombination thereof, either alone or with promoters such as W, Mo, Au,Ag, Cr, Zn, Mn, Sn, B, P, Bi, and alloys or any combination thereof.Other effective hydrogenation catalyst materials include eithersupported nickel or ruthenium modified with rhenium. In an embodiment,the hydrogenation catalyst also includes any one of the supports,depending on the desired functionality of the catalyst. Thehydrogenation catalysts may be prepared by methods known to those ofordinary skill in the art.

In some embodiments the hydrogenation catalyst includes a supportedGroup VIII metal catalyst and a metal sponge material (e.g., a spongenickel catalyst). Raney nickel provides an example of an activatedsponge nickel catalyst suitable for use in this invention. In otherembodiment, the hydrogenation reaction in the invention is performedusing a catalyst comprising a nickel-rhenium catalyst or atungsten-modified nickel catalyst. One example of a suitable catalystfor the hydrogenation reaction of the invention is a carbon-supportednickel-rhenium catalyst.

In an embodiment, a suitable Raney nickel catalyst may be prepared bytreating an alloy of approximately equal amounts by weight of nickel andaluminum with an aqueous alkali solution, e.g., containing about 25weight % of sodium hydroxide. The aluminum is selectively dissolved bythe aqueous alkali solution resulting in a sponge shaped materialcomprising mostly nickel with minor amounts of aluminum. The initialalloy includes promoter metals (i.e., molybdenum or chromium) in theamount such that about 1 to 2 weight % remains in the formed spongenickel catalyst. In another embodiment, the hydrogenation catalyst isprepared using a solution of ruthenium (III) nitrosylnitrate, ruthenium(III) chloride in water to impregnate a suitable support material. Thesolution is then dried to form a solid having a water content of lessthan about 1% by weight. The solid may then be reduced at atmosphericpressure in a hydrogen stream at 300° C. (uncalcined) or 400° C.(calcined) in a rotary ball furnace for 4 hours. After cooling andrendering the catalyst inert with nitrogen, 5% by volume of oxygen innitrogen is passed over the catalyst for 2 hours.

In certain embodiments, the catalyst described includes a catalystsupport. The catalyst support stabilizes and supports the catalyst. Thetype of catalyst support used depends on the chosen catalyst and thereaction conditions. Suitable supports for the invention include, butare not limited to, carbon, silica, silica-alumina, zirconia, titania,ceria, vanadia, nitride, boron nitride, heteropolyacids, hydroxyapatite,zinc oxide, chromia, zeolites, carbon nanotubes, carbon fullerene andany combination thereof.

The catalysts used in this invention can be prepared using conventionalmethods known to those in the art. Suitable methods may include, but arenot limited to, incipient wetting, evaporative impregnation, chemicalvapor deposition, wash-coating, magnetron sputtering techniques, and thelike.

The conditions for which to carry out the hydrogenation reaction willvary based on the type of starting material and the desired products.One of ordinary skill in the art, with the benefit of this disclosure,will recognize the appropriate reaction conditions. In general, thehydrogenation reaction is conducted at temperatures of 80° C. to 250°C., and preferably at 90° C. to 200° C., and most preferably at 100° C.to 150° C. In some embodiments, the hydrogenation reaction is conductedat pressures from 500 KPa to 14000 KPa.

The hydrogen used in the hydrogenolysis reaction of the currentinvention may include external hydrogen, recycled hydrogen, in situgenerated hydrogen, and any combination thereof. As used herein, theterm “external hydrogen” refers to hydrogen that does not originate fromthe biomass reaction itself, but rather is added to the system fromanother source.

In some embodiments of the invention, it is desirable to convert thestarting carbohydrate to a smaller molecule that will be more readilyconverted to desired higher hydrocarbons. One suitable method for thisconversion is through a hydrogenolysis reaction. Various processes areknown for performing hydrogenolysis of carbohydrates. One suitablemethod includes contacting a carbohydrate with hydrogen or hydrogenmixed with a suitable gas and a hydrogenolysis catalyst in ahydrogenolysis reactor under conditions sufficient to form a reactionproduct comprising smaller molecules or polyols. As used herein, theterm “smaller molecules or polyols” includes any molecule that has asmaller molecular weight, which can include a smaller number of carbonatoms or oxygen atoms than the starting carbohydrate. In an embodiment,the reaction products include smaller molecules that include polyols andalcohols. Someone of ordinary skill in the art would be able to choosethe appropriate method by which to carry out the hydrogenolysisreaction.

In some embodiments, a 5 and/or 6 carbon sugar or sugar alcohol may beconverted to propylene glycol, ethylene glycol, and glycerol using ahydrogenolysis catalyst. The hydrogenolysis catalyst may include Cr, Mo,W, Re, Mn, Cu, Cd, Fe, Co, Ni, Pt, Pd, Rh, Ru, Ir, Os, and alloys or anycombination thereof, either alone or with promoters such as Au, Ag, Cr,Zn, Mn, Sn, Bi, B, O, and alloys or any combination thereof. Thehydrogenolysis catalyst may also include a carbonaceous pyropolymercatalyst containing transition metals (e.g., chromium, molybdenum,tungsten, rhenium, manganese, copper, cadmium) or Group VIII metals(e.g., iron, cobalt, nickel, platinum, palladium, rhodium, ruthenium,iridium, and osmium). In certain embodiments, the hydrogenolysiscatalyst may include any of the above metals combined with an alkalineearth metal oxide or adhered to a catalytically active support. Incertain embodiments, the catalyst described in the hydrogenolysisreaction may include a catalyst support as described above for thehydrogenation reaction.

The conditions for which to carry out the hydrogenolysis reaction willvary based on the type of starting material and the desired products.One of ordinary skill in the art, with the benefit of this disclosure,will recognize the appropriate conditions to use to carry out thereaction. In general, they hydrogenolysis reaction is conducted attemperatures of 110° C. to 300° C., and preferably at 170° C. to 220°C., and most preferably at 200° C. to 225° C. In some embodiments, thehydrogenolysis reaction is conducted under basic conditions, preferablyat a pH of 8 to 13, and even more preferably at a pH of 10 to 12. Insome embodiments, the hydrogenolysis reaction is conducted at pressuresin a range between 60 KPa and 16500 KPa, and preferably in a rangebetween 1700 KPa and 14000 KPa, and even more preferably between 4800KPa and 11000 KPa.

The hydrogen used in the hydrogenolysis reaction of the currentinvention can include external hydrogen, recycled hydrogen, in situgenerated hydrogen, and any combination thereof.

In some embodiments, the reaction products discussed above may beconverted into higher hydrocarbons through a condensation reaction in acondensation reactor. In such embodiments, condensation of the reactionproducts occurs in the presence of a catalyst capable of forming higherhydrocarbons. While not intending to be limited by theory, it isbelieved that the production of higher hydrocarbons proceeds through astepwise addition reaction including the formation of carbon-carbon, orcarbon-oxygen bond. The resulting reaction products include any numberof compounds containing these moieties, as described in more detailbelow.

In certain embodiments, suitable condensation catalysts include an acidcatalyst, a base catalyst, or an acid/base catalyst. As used herein, theterm “acid/base catalyst” refers to a catalyst that has both an acid anda base functionality. In some embodiments the condensation catalyst caninclude, without limitation, zeolites, carbides, nitrides, zirconia,alumina, silica, aluminosilicates, phosphates, titanium oxides, zincoxides, vanadium oxides, lanthanum oxides, yttrium oxides, scandiumoxides, magnesium oxides, cerium oxides, barium oxides, calcium oxides,hydroxides, heteropolyacids, inorganic acids, acid modified resins, basemodified resins, and any combination thereof. In some embodiments, thecondensation catalyst can also include a modifier. Suitable modifiersinclude La, Y, Sc, P, B, Bi, Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba, and anycombination thereof. In some embodiments, the condensation catalyst canalso include a metal. Suitable metals include Cu, Ag, Au, Pt, Ni, Fe,Co, Ru, Zn, Cd, Ga, In, Rh, Pd, Ir, Re, Mn, Cr, Mo, W, Sn, Os, alloys,and any combination thereof.

In certain embodiments, the catalyst described in the condensationreaction may include a catalyst support as described above for thehydrogenation reaction. In certain embodiments, the condensationcatalyst is self-supporting. As used herein, the term “self-supporting”means that the catalyst does not need another material to serve assupport. In other embodiments, the condensation catalyst in used inconjunction with a separate support suitable for suspending thecatalyst. In an embodiment, the condensation catalyst support is silica.

The conditions under which the condensation reaction occurs will varybased on the type of starting material and the desired products. One ofordinary skill in the art, with the benefit of this disclosure, willrecognize the appropriate conditions to use to carry out the reaction.In some embodiments, the condensation reaction is carried out at atemperature at which the thermodynamics for the proposed reaction arefavorable. The temperature for the condensation reaction will varydepending on the specific starting polyol or alcohol. In someembodiments, the temperature for the condensation reaction is in a rangefrom 80° C. to 500° C., and preferably from 125° C. to 450° C., and mostpreferably from 125° C. to 250° C. In some embodiments, the condensationreaction is conducted at pressures in a range between 0 Kpa to 9000 KPa,and preferably in a range between 0 KPa and 7000 KPa, and even morepreferably between 0 KPa and 5000 KPa.

The higher alkanes formed by the invention include, but are not limitedto, branched or straight chain alkanes that have from 4 to 30 carbonatoms, branched or straight chain alkenes that have from 4 to 30 carbonatoms, cycloalkanes that have from 5 to 30 carbon atoms, cycloalkenesthat have from 5 to 30 carbon atoms, aryls, fused aryls, alcohols, andketones. Suitable alkanes include, but are not limited to, butane,pentane, pentene, 2-methylbutane, hexane, hexene, 2-methylpentane,3-methylpentane, 2,2,-dimethylbutane, 2,3-dimethylbutane, heptane,heptene, octane, octene, 2,2,4-trimethylpentane, 2,3-dimethyl hexane,2,3,4-trimethylpentane, 2,3-dimethylpentane, nonane, nonene, decane,decene, undecane, undecene, dodecane, dodecene, tridecane, tridecene,tetradecane, tetradecene, pentadecane, pentadecene, nonyldecane,nonyldecene, eicosane, eicosene, uneicosane, uneicosene, doeicosane,doeicosene, trieicosane, trieicosene, tetraeicosane, tetraeicosene, andisomers thereof. Some of these products may be suitable for use asfuels.

In some embodiments, the cycloalkanes and the cycloalkenes areunsubstituted. In other embodiments, the cycloalkanes and cycloalkenesare mono-substituted. In still other embodiments, the cycloalkanes andcycloalkenes are multi-substituted. In the embodiments comprising thesubstituted cycloalkanes and cycloalkenes, the substituted groupincludes, without limitation, a branched or straight chain alkyl having1 to 12 carbon atoms, a branched or straight chain alkylene having 1 to12 carbon atoms, a phenyl, and any combination thereof. Suitablecycloalkanes and cycloalkenes include, but are not limited to,cyclopentane, cyclopentene, cyclohexane, cyclohexene,methyl-cyclopentane, methyl-cyclopentene, ethyl-cyclopentane,ethyl-cyclopentene, ethyl-cyclohexane, ethyl-cyclohexene, isomers andany combination thereof.

In some embodiments, the aryls formed are unsubstituted. In anotherembodiment, the aryls formed are mono-substituted. In the embodimentscomprising the substituted aryls, the substituted group includes,without limitation, a branched or straight chain alkyl having 1 to 12carbon atoms, a branched or straight chain alkylene having 1 to 12carbon atoms, a phenyl, and any combination thereof. Suitable aryls forthe invention include, but are not limited to, benzene, toluene, xylene,ethyl benzene, para xylene, meta xylene, and any combination thereof.

The alcohols produced in the invention have from 4 to 30 carbon atoms.In some embodiments, the alcohols are cyclic. In other embodiments, thealcohols are branched. In another embodiment, the alcohols are straightchained. Suitable alcohols for the invention include, but are notlimited to, butanol, pentanol, hexanol, heptanol, octanol, nonanol,decanol, undecanol, dodecanol, tridecanol, tetradecanol, pentadecanol,hexadecanol, heptyldecanol, octyldecanol, nonyldecanol, eicosanol,uneicosanol, doeicosanol, trieicosanol, tetraeicosanol, and isomersthereof.

The ketones produced in the invention have from 4 to 30 carbon atoms. Inan embodiment, the ketones are cyclic. In another embodiment, theketones are branched. In another embodiment, the ketones are straightchained. Suitable ketones for the invention include, but are not limitedto, butanone, pentanone, hexanone, heptanone, octanone, nonanone,decanone, undecanone, dodecanone, tridecanone, tetradecanone,pentadecanone, hexadecanone, heptyldecanone, octyldecanone,nonyldecanone, eicosanone, uneicosanone, doeicosanone, trieicosanone,tetraeicosanone, and isomers thereof.

Another such chemical modification is interesterification. Naturallyproduced glycerolipids do not have a uniform distribution of fatty acidconstituents. In the context of oils, interesterification refers to theexchange of acyl radicals between two esters of different glycerolipids.The interesterification process provides a mechanism by which the fattyacid constituents of a mixture of glycerolipids can be rearranged tomodify the distribution pattern. Interesterification is a well-knownchemical process, and generally comprises heating (to about 200° C.) amixture of oils for a period (e.g., 30 minutes) in the presence of acatalyst, such as an alkali metal or alkali metal alkylate (e.g., sodiummethoxide). This process can be used to randomize the distributionpattern of the fatty acid constituents of an oil mixture, or can bedirected to produce a desired distribution pattern. This method ofchemical modification of lipids can be performed on materials providedherein, such as microbial biomass with a percentage of dry cell weightas lipid at least 20%.

Directed interesterification, in which a specific distribution patternof fatty acids is sought, can be performed by maintaining the oilmixture at a temperature below the melting point of some TAGs whichmight occur. This results in selective crystallization of these TAGs,which effectively removes them from the reaction mixture as theycrystallize. The process can be continued until most of the fatty acidsin the oil have precipitated, for example. A directedinteresterification process can be used, for example, to produce aproduct with a lower calorie content via the substitution oflonger-chain fatty acids with shorter-chain counterparts. Directedinteresterification can also be used to produce a product with a mixtureof fats that can provide desired melting characteristics and structuralfeatures sought in food additives or products (e.g., margarine) withoutresorting to hydrogenation, which can produce unwanted trans isomers.

Interesterification of oils produced by the methods described herein canbe performed in conjunction with one or more of the methods and/ormaterials, or to produce products, as reported in the following: U.S.Pat. No. 6,080,853 (Nondigestible fat substitutes); U.S. Pat. No.4,288,378 (Peanut butter stabilizer); U.S. Pat. No. 5,391,383 (Ediblespray oil); U.S. Pat. No. 6,022,577 (Edible fats for food products);U.S. Pat. No. 5,434,278 (Edible fats for food products); U.S. Pat. No.5,268,192 (Low calorie nut products); U.S. Pat. No. 5,258,197 (Reducecalorie edible compositions); U.S. Pat. No. 4,335,156 (Edible fatproduct); U.S. Pat. No. 7,288,278 (Food additives or medicaments); U.S.Pat. No. 7,115,760 (Fractionation process); U.S. Pat. No. 6,808,737(Structural fats); U.S. Pat. No. 5,888,947 (Engine lubricants); U.S.Pat. No. 5,686,131 (Edible oil mixtures); and U.S. Pat. No. 4,603,188(Curable urethane compositions).

In one embodiment in accordance with the invention, transesterificationof the oil, as described above, is followed by reaction of thetransesterified product with polyol, as reported in U.S. Pat. No.6,465,642, to produce polyol fatty acid polyesters. Such anesterification and separation process may comprise the steps as follows:reacting a lower alkyl ester with polyol in the presence of soap;removing residual soap from the product mixture; water-washing anddrying the product mixture to remove impurities; bleaching the productmixture for refinement; separating at least a portion of the unreactedlower alkyl ester from the polyol fatty acid polyester in the productmixture; and recycling the separated unreacted lower alkyl ester.

Transesterification can also be performed on microbial biomass withshort chain fatty acid esters, as reported in U.S. Pat. No. 6,278,006.In general, transesterification may be performed by adding a short chainfatty acid ester to an oil in the presence of a suitable catalyst andheating the mixture. In some embodiments, the oil comprises about 5% toabout 90% of the reaction mixture by weight. In some embodiments, theshort chain fatty acid esters can be about 10% to about 50% of thereaction mixture by weight. Non-limiting examples of catalysts includebase catalysts, sodium methoxide, acid catalysts including inorganicacids such as sulfuric acid and acidified clays, organic acids such asmethane sulfonic acid, benzenesulfonic acid, and toluenesulfonic acid,and acidic resins such as Amberlyst 15. Metals such as sodium andmagnesium, and metal hydrides also are useful catalysts.

Another such chemical modification is hydroxylation, which involves theaddition of water to a double bond resulting in saturation and theincorporation of a hydroxyl moiety. The hydroxylation process provides amechanism for converting one or more fatty acid constituents of aglycerolipid to a hydroxy fatty acid. Hydroxylation can be performed,for example, via the method reported in U.S. Pat. No. 5,576,027.Hydroxylated fatty acids, including castor oil and its derivatives, areuseful as components in several industrial applications, including foodadditives, surfactants, pigment wetting agents, defoaming agents, waterproofing additives, plasticizing agents, cosmetic emulsifying and/ordeodorant agents, as well as in electronics, pharmaceuticals, paints,inks, adhesives, and lubricants. One example of how the hydroxylation ofa glyceride may be performed is as follows: fat may be heated,preferably to about 30-50° C. combined with heptane and maintained attemperature for thirty minutes or more; acetic acid may then be added tothe mixture followed by an aqueous solution of sulfuric acid followed byan aqueous hydrogen peroxide solution which is added in small incrementsto the mixture over one hour; after the aqueous hydrogen peroxide, thetemperature may then be increased to at least about 60° C. and stirredfor at least six hours; after the stirring, the mixture is allowed tosettle and a lower aqueous layer formed by the reaction may be removedwhile the upper heptane layer formed by the reaction may be washed withhot water having a temperature of about 60° C.; the washed heptane layermay then be neutralized with an aqueous potassium hydroxide solution toa pH of about 5 to 7 and then removed by distillation under vacuum; thereaction product may then be dried under vacuum at 100° C. and the driedproduct steam-deodorized under vacuum conditions and filtered at about50° to 60° C. using diatomaceous earth.

Hydroxylation of microbial oils produced by the methods described hereincan be performed in conjunction with one or more of the methods and/ormaterials, or to produce products, as reported in the following: U.S.Pat. No. 6,590,113 (Oil-based coatings and ink); U.S. Pat. No. 4,049,724(Hydroxylation process); U.S. Pat. No. 6,113,971 (Olive oil butter);U.S. Pat. No. 4,992,189 (Lubricants and lube additives); U.S. Pat. No.5,576,027 (Hydroxylated milk); and U.S. Pat. No. 6,869,597 (Cosmetics).

Hydroxylated glycerolipids can be converted to estolides. Estolidesconsist of a glycerolipid in which a hydroxylated fatty acid constituenthas been esterified to another fatty acid molecule. Conversion ofhydroxylated glycerolipids to estolides can be carried out by warming amixture of glycerolipids and fatty acids and contacting the mixture witha mineral acid, as described by Isbell et al., JAOCS 71(2):169-174(1994). Estolides are useful in a variety of applications, includingwithout limitation those reported in the following: U.S. Pat. No.7,196,124 (Elastomeric materials and floor coverings); U.S. Pat. No.5,458,795 (Thickened oils for high-temperature applications); U.S. Pat.No. 5,451,332 (Fluids for industrial applications); U.S. Pat. No.5,427,704 (Fuel additives); and U.S. Pat. No. 5,380,894 (Lubricants,greases, plasticizers, and printing inks).

Another such chemical modification is olefin metathesis. In olefinmetathesis, a catalyst severs the alkylidene carbons in an alkene(olefin) and forms new alkenes by pairing each of them with differentalkylidine carbons. The olefin metathesis reaction provides a mechanismfor processes such as truncating unsaturated fatty acid alkyl chains atalkenes by ethenolysis, cross-linking fatty acids through alkenelinkages by self-metathesis, and incorporating new functional groups onfatty acids by cross-metathesis with derivatized alkenes.

In conjunction with other reactions, such as transesterification andhydrogenation, olefin metathesis can transform unsaturated glycerolipidsinto diverse end products. These products include glycerolipid oligomersfor waxes; short-chain glycerolipids for lubricants; homo- andhetero-bifunctional alkyl chains for chemicals and polymers; short-chainesters for biofuel; and short-chain hydrocarbons for jet fuel. Olefinmetathesis can be performed on triacylglycerols and fatty acidderivatives, for example, using the catalysts and methods reported inU.S. Pat. No. 7,119,216, US Patent Pub. No. 2010/0160506, and U.S.Patent Pub. No. 2010/0145086.

Olefin metathesis of bio-oils generally comprises adding a solution ofRu catalyst at a loading of about 10 to 250 ppm under inert conditionsto unsaturated fatty acid esters in the presence (cross-metathesis) orabsence (self-metathesis) of other alkenes. The reactions are typicallyallowed to proceed from hours to days and ultimately yield adistribution of alkene products. One example of how olefin metathesismay be performed on a fatty acid derivative is as follows: A solution ofthe first generation Grubbs Catalyst(dichloro[2(1-methylethoxy-α-O)phenyl]methylene-α-C](tricyclohexyl-phosphine) in toluene at a catalyst loading of 222 ppmmay be added to a vessel containing degassed and dried methyl oleate.Then the vessel may be pressurized with about 60 psig of ethylene gasand maintained at or below about 30° C. for 3 hours, wherebyapproximately a 50% yield of methyl 9-decenoate may be produced.

Olefin metathesis of oils produced by the methods described herein canbe performed in conjunction with one or more of the methods and/ormaterials, or to produce products, as reported in the following: PatentApp. PCT/US07/081427 (α-olefin fatty acids) and U.S. patent applicationSer. No. 12/281,938 (petroleum creams), Ser. No. 12/281,931 (paintballgun capsules), Ser. No. 12/653,742 (plasticizers and lubricants), Ser.No. 12/422,096 (bifunctional organic compounds), and Ser. No. 11/795,052(candle wax).

Other chemical reactions that can be performed on microbial oils includereacting triacylglycerols with a cyclopropanating agent to enhancefluidity and/or oxidative stability, as reported in U.S. Pat. No.6,051,539; manufacturing of waxes from triacylglycerols, as reported inU.S. Pat. No. 6,770,104; and epoxidation of triacylglycerols, asreported in “The effect of fatty acid composition on the acrylationkinetics of epoxidized triacylglycerols”, Journal of the American OilChemists' Society, 79:1, 59-63, (2001) and Free Radical Biology andMedicine, 37:1, 104-114 (2004).

The generation of oil-bearing microbial biomass for fuel and chemicalproducts as described above results in the production of delipidatedbiomass meal. Delipidated meal is a byproduct of preparing algal oil andis useful as animal feed for farm animals, e.g., ruminants, poultry,swine and aquaculture. The resulting meal, although of reduced oilcontent, still contains high quality proteins, carbohydrates, fiber,ash, residual oil and other nutrients appropriate for an animal feed.Because the cells are predominantly lysed by the oil separation process,the delipidated meal is easily digestible by such animals. Delipidatedmeal can optionally be combined with other ingredients, such as grain,in an animal feed. Because delipidated meal has a powdery consistency,it can be pressed into pellets using an extruder or expander or anothertype of machine, which are commercially available.

The invention, having been described in detail above, is exemplified inthe following examples, which are offered to illustrate, but not tolimit, the claimed invention.

XIV. EXAMPLES Example 1 Fatty Acid Analysis by Fatty Acid Methyl EsterDetection

Lipid samples were prepared from dried biomass. 20-40 mg of driedbiomass was resuspended in 2 mL of 5% H₂SO₄ in MeOH, and 200 ul oftoluene containing an appropriate amount of a suitable internal standard(C19:0) was added. The mixture was sonicated briefly to disperse thebiomass, then heated at 70-75° C. for 3.5 hours. 2 mL of heptane wasadded to extract the fatty acid methyl esters, followed by addition of 2mL of 6% K₂CO₃ (aq) to neutralize the acid. The mixture was agitatedvigorously, and a portion of the upper layer was transferred to a vialcontaining Na₂SO₄ (anhydrous) for gas chromatography analysis usingstandard FAME GC/FID (fatty acid methyl ester gas chromatography flameionization detection) methods. Fatty acid profiles reported below weredetermined by this method.

Example 2 Triacylglyceride Purification from Oil and Methods forTriacylglyceride Lipase Digestion

The triacylglyceride (TAG) fraction of each oil sample was isolated bydissolving ˜10 mg of oil in dichloromethane and loading it onto aBond-Elut aminopropyl solid-phase extraction cartridge (500 mg)preconditioned with heptane. TAGs were eluted with dicholoromethane-MeOH(1:1) into a collection tube, while polar lipids were retained on thecolumn. The solvent was removed with a stream of nitrogen gas. Trisbuffer and 2 mg porcine pancreatic lipase (Type II, Sigma, 100-400units/mg) were added to the TAG fraction, followed by addition of bilesalt and calcium chloride solutions. The porcine pancreatic lipasecleaves sn-1 and sn-3 fatty acids, thereby generating2-monoacylglycerides and free fatty acids. This mixture was heated withagitation at 40° C. for three minutes, cooled briefly, then quenchedwith 6 N HCl. The mixture was then extracted with diethyl ether and theether layer was washed with water then dried over sodium sulfate. Thesolvent was removed with a stream of nitrogen. To isolate themonoacylglyceride (MAG) fraction, the residue was dissolved in heptaneand loaded onto a second aminopropyl solid phase extraction cartridgepretreated with heptane. Residual TAGs were eluted with diethylether-dichloromethane-heptane (1:9:40), diacylglycerides (DAGs) wereeluted with ethyl acetate-heptane (1:4), and MAGs were eluted from thecartridge with dichloromethane-methanol (2:1). The resulting MAG, DAG,and TAG fractions were then concentrated to dryness with a stream ofnitrogen and subjected to routine direct transesterification method ofGC/FID analysis as described in Example 1.

Example 3 Engineering Microorganisms for Fatty Acid and SN-2 ProfilesIncreased in Lauric Acid Through Exogenous LPAAT Expression

This example describes the use of recombinant polynucleotides thatencode a C. nucifera 1-acyl-sn-glycerol-3-phosphate acyltransferase (CnLPAAT) enzyme to engineer a microorganism in which the fatty acidprofile and the sn-2 profile of the transformed microorganism has beenenriched in lauric acid.

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain A, was initially transformed with the plasmid construct pSZ1283according to biolistic transformation methods as described inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. pSZ1283, described inPCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696 herebyincorporated by reference, comprised the coding sequence of the Cupheawrightii FATB2 (CwTE2) thioesterase (SEQ ID NO: 10), 5′ (SEQ ID NO: 1)and 3′ (SEQ ID NO: 2) homologous recombination targeting sequences(flanking the construct) to the 6S genomic region for integration intothe nuclear genome, and a S. cerevisiae suc2 sucrose invertase codingregion (SEQ ID NO: 4), to express the protein sequence given in SEQ IDNO: 3, under the control of C. reinhardtii β-tubulin promoter/5′UTR (SEQID NO: 5) and Chlorella vulgaris nitrate reductase 3′ UTR (SEQ ID NO:6). This S. cerevisiae suc2 expression cassette is listed as SEQ ID NO:7 and served as a selectable marker. The CwTE2 protein coding sequenceto express the protein sequence given in SEQ ID NO: 11, was under thecontrol of the P. moriformis Amt03 promoter/5′UTR (SEQ ID NO: 8) and C.vulgaris nitrate reductase 3′UTR. The protein coding regions of CwTE2and suc2 were codon optimized to reflect the codon bias inherent in P.moriformis UTEX 1435 nuclear genes as described in PCT/U52009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696.

Upon transformation of pSZ1283 into Strain A, positive clones wereselected on agar plates with sucrose as the sole carbon source. Primarytransformants were then clonally purified and a single transformant,Strain B, was selected for further genetic modification. Thisgenetically engineered strain was transformed with plasmid constructpSZ2046 to interrupt the pLoop genomic locus of Strain B. ConstructpSZ2046 comprised the coding sequence of the C. nucifera1-acyl-sn-glycerol-3-phosphate acyltransferase (Cn LPAAT) enzyme (SEQ IDNO: 12), 5′ (SEQ ID NO: 13) and 3′ (SEQ ID NO: 14) homologousrecombination targeting sequences (flanking the construct) to the pLoopgenomic region for integration into the nuclear genome, and a neomycinresistance protein-coding sequence under the control of C. reinhardtiiβ-tubulin promoter/5′UTR (SEQ ID NO: 5), and Chlorella vulgaris nitratereductase 3′ UTR (SEQ ID NO: 6). This NeoR expression cassette is listedas SEQ ID NO: 15 and served as a selectable marker. The Cn LPAAT proteincoding sequence was under the control of the P. moriformis Amt03promoter/5′UTR (SEQ ID NO: 8) and C. vulgaris nitrate reductase 3′UTR.The protein coding regions of Cn LPAAT and NeoR were codon optimized toreflect the codon bias inherent in P. moriformis UTEX 1435 nuclear genesas described in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. The amino acid sequence of CnLPAAT is provided as SEQ ID NO: 16.

Upon transformation of pSZ2046 into Strain B, thereby generating StrainC, positive clones were selected on agar plates comprising G418(Geneticin). Individual transformants were clonally purified and grownat pH 7.0 under conditions suitable for lipid production as detailed inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples were preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples were analyzed using standard fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1.The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis UTEX 1435 (U1) grown on glucose as asole carbon source, untransformed Strain B and five pSZ2046 positivetransformants (Strain C, 1-5) are presented in Table 6.

TABLE 6 Effect of LPAAT expression on fatty acid profiles of transformedPrototheca moriformis (UTEX 1435) comprising a mid-chain preferringthioesterase. Area % Fatty Strain Strain Strain Strain Strain Strainacid U1 B C-1 C-2 C-3 C-4 C-5 C10:0  0.01  5.53 11.37 11.47 10.84 11.1311.12 C12:0  0.04 31.04 46.63 46.47 45.84 45.80 45.67 C14:0  1.27 15.9915.14 15.12 15.20 15.19 15.07 C16:0 27.20 12.49  7.05  7.03  7.30  7.20 7.19 C18:0  3.85  1.30  0.71  0.72  0.74  0.74  0.74 C18:1 58.70 24.3910.26 10.41 10.95 11.31 11.45 C18:2  7.18  7.79  7.05  6.93  7.30  6.88 7.01 C10-  0.50 36.57 58.00 57.94 56.68 56.93 56.79 C12

As shown in Table 6, the fatty acid profile of Strain B expressing CwTE2showed increased composition of C10:0, C12:0, and C14:0 fatty acids anda decrease in C16:0, C18:0, and C18:1 fatty acids relative to the fattyacid profile of the untransformed UTEX 1435 strain. The impact ofadditional genetic modification on the fatty acid profile of thetransformed strains, namely the expression of CnLPAAT in Strain B, is astill further increase in the composition of C10:0 and C12:0 fattyacids, a still further decrease in C16:0, C18:0, and C18:1 fatty acids,but no significant effect on the C14:0 fatty acid composition. Thesedata indicate that the CnLPAAT shows substrate preference in the contextof a microbial host organism.

The untransformed P. moriformis Strain A is characterized by a fattyacid profile comprising less than 0.5% C12 fatty acids and less than 1%C10-C12 fatty acids. In contrast, the fatty acid profile of Strain Bexpressing a C. wrightii thioesterase comprised 31% C12:0 fatty acids,with C10-C12 fatty acids comprising greater than 36% of the total fattyacids. Further, fatty acid profiles of Strain C, expressing a higherplant thioesterase and a CnLPAAT enzyme, comprised between 45.67% and46.63% C12:0 fatty acids, with C10-C12% fatty acids comprising between71 and 73% of total fatty acids. The result of expressing an exogenousthioesterase was a 62-fold increase in the percentage of C12 fatty acidpresent in the engineered microbe. The result of expressing an exogenousthioesterase and exogenous LPAAT was a 92-fold increase in thepercentage of C12 fatty acids present in the engineered microbe.

The TAG fraction of oil samples extracted from Strains A, B, and C wereanalyzed for the sn-2 profile of their triacylglycerides. The TAGs wereextracted and processed as described in Example 2 and analyzed as inExamples 1 and 2. The fatty acid composition and the sn-2 profiles ofthe TAG fraction of oil extracted from Strains A, B, and C (expressed asArea % of total fatty acids) are presented in Table 7. Values notreported are indicated as “n.r.”

TABLE 7 Effect of LPAAT expression on the fatty acid composition and thesn-2 profile of TAGs produced from transformed Prototheca moriformis(UTEX 1435) comprising a mid-chain preferring thioesterase. Strain AreaStrain C % Strain A Strain B (pSZ1500 + fatty (untransformed) (pSZ1500)pSZ2046) acid FA sn-2 profile FA sn-2 profile FA sn-2 profile C10:0 n.r.n.r. 11.9 14.2 12.4 7.1 C12:0 n.r. n.r. 42.4 25 47.9 52.8 C14:0 1.0 0.612 10.4 13.9 9.1 C16:0 23.9 1.6 7.2 1.3 6.1 0.9 C18:0 3.7 0.3 n.r n.r.0.8 0.3 C18:1 64.3 90.5 18.3 36.6 9.9 17.5 C18:2 4.5 5.8 5.8 10.8 6.5 10C18:3 n.r. n.r. n.r. n.r. 1.1 1.6

As shown in Table 7, the fatty acid composition of triglycerides (TAGs)isolated from Strain B expressing CwTE2 was increased for C10:0, C12:0,and C14:0 fatty acids and decrease in C16:0 and C18:1 fatty acidsrelative to the fatty acid profile of TAGs isolated from untransformedStrain A. The impact of additional genetic modification on the fattyacid profile of the transformed strains, namely the expression ofCnLPAAT, was a still further increase in the composition of C10:0 andC12:0 fatty acids, a still further decrease in C16:0, C18:0, and C18:1fatty acids, but no significant effect on the C14:0 fatty acidcomposition. These data indicate that expression of the exogenousCnLPAAT improves the midchain fatty acid profile of transformedmicrobes.

The untransformed P. moriformis Strain A is characterized by an sn-2profile of about 0.6% C14, about 1.6% C16:0, about 0.3% C18:0, about 90%C18:1, and about 5.8% C18:2. In contrast to Strain A, Strain B,expressing a C. wrightii thioesterase is characterized by an sn-2profile that is higher in midchain fatty acids and lower in long chainfatty acids. C12 fatty acids comprised 25% of the sn-2 profile of StrainB. The impact of additional genetic modification on the sn-2 profile ofthe transformed strains, namely the expression of CnLPAAT, was still afurther increase in C12 fatty acids (from 25% to 52.8%), a decrease inC18:1 fatty acids (from 36.6% to 17.5%), and a decrease in C10:0 fattyacids. (The sn-2 profile composition of C14:0 and C16:0 fatty acids wasrelatively similar for Strains B and C.)

These data demonstrate the utility and effectiveness of polynucleotidespermitting exogenous LPAAT expression to alter the fatty acid profile ofengineered microorganisms, and in particular in increasing theconcentration of C10:0 and C12:0 fatty acids in microbial cells. Thesedata further demonstrate the utility and effectiveness ofpolynucleotides permitting exogenous thioesterase and exogenous LPAATexpression to alter the sn-2 profile of TAGs produced by microbialcells, in particular in increasing the C12 composition of sn-2 profilesand decreasing the C18:1 composition of sn-2 profiles.

Example 4 Thermal Behavior of Oils Produced from Recombinant Microalgae

FIGS. 1-14 include fatty acid profiles and melting curves of refined,bleached and deodorized oils from genetically engineered Protothecamoriformis strains. In some cases, modifications of the melting curvesare obtained via genetic engineering. For example, some of the oilsproduced have shallower or sharper melting transitions relative tocontrol microalgal oils (i.e., those produced from strains lacking agiven genetic modification) or relative to widely available plant oils.In addition, FIG. 12 shows scanning calorimetry for a high palmitic oilwhen tempered by holding at room temperature for several days (lowertrace) and for the same oil after performing the first scan (uppertrace). The scans ranged from −60° C. to +50° C. with a heating rate of10° C/minute. The differences between the two traces suggests thattempering of the oil caused a change in crystal structure within theoil.

Also of note, FIGS. 10 and 11 show stability testing of RBD-5 and RBD 6.Remarkably, RBD-6, an oil with less than 0.1% 18:2 and 18:3 fatty acidswas substantially stable as measured by the oxidative stability index(AOCS Method Cd 12b-92) even after 36 hours of heating at 110° C.

Table 8, below, gives details of the genetic engineering of the strainsidentified in FIGS. 1-13.

TABLE 8 Genetically engineered strains. RB Z Ulmus Americanathioesterase RBD-1 Cuphea wrightii FATB2 thioesterase driven by amt03RBD-2 Ulmus americana thioesterase RBD-3 Native C. hookerianaC16:0-specific thioesterase with amt03 promoter RBD Y Ulmus Americanathioesterase with Btub promoter RBD X SAD2B knockout with native Cwrightii FAT2B thioesterase, amt03 promoter RBD W SAD2B KO with NativeC. wrightii FATB2 driven by amt03 at insertion site RBD-4 control strainRBD-5 FATA-1 knockout with Carthamus oleate sp. TE driven by amt03promoter at insertion site RBD-6 FADc knockout with Carthamus tinctoriusoleoyl thioesterase

Example 5 Characteristics of Processed Oil Produced from EngineeredMicroorganisms

Methods and effects of transforming Prototheca moriformis (UTEX 1435)with transformation vector pSZ1500 (SEQ ID NO: 17) have been previouslydescribed in PCT Application Nos. PCT/US2011/038463, PCT/US2011/038464,and PCT/US2012/023696.

A classically mutagenized (for higher oil production) derivative ofPrototheca moriformis (UTEX 1435), Strain A, was transformed withpSZ1500 according to biolistic transformation methods as described inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. pSZ1500 comprised nucleotidesequence of the Carthamus tinctorius oleyl-thioesterase (CtOTE) gene,codon-optimized for expression in P. moriformis UTEX 1435. The pSZ1500expression construct included 5′ (SEQ ID NO: 18) and 3′ (SEQ ID NO: 19)homologous recombination targeting sequences (flanking the construct) tothe FADc genomic region for integration into the nuclear genome and a S.cerevisiae suc2 sucrose invertase coding region under the control of C.reinhardtii β-tubulin promoter/5′UTR (SEQ ID NO: 5) and Chlorellavulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). This S. cerevisiaesuc2 expression cassette is listed as SEQ ID NO: 7 and served as aselection marker. The CtOTE coding region was under the control of theP. moriformis Amt03 promoter/5′UTR (SEQ ID NO: 8) and C. vulgarisnitrate reductase 3′UTR, and the native transit peptide was replacedwith the C. protothecoides stearoyl-ACP desaturase transit peptide (SEQID NO: 9). The protein coding regions of CtOTE and suc2 were codonoptimized to reflect the codon bias inherent in P. moriformis UTEX 1435nuclear genes as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696.

Primary pSZ1500 transformants of Strain A were selected on agar platescontaining sucrose as a sole carbon source, clonally purified, and asingle engineered line, Strain D was selected for analysis. Strain D wasgrown as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696. Hexaneextraction of the oil from the generated biomass was then performedusing standard methods, and the resulting triglyceride oil wasdetermined to be free of residual hexane. Other methods of extraction ofoil from microalgae using an expeller press are described in PCTApplication No. PCT/US2010/031108 and are hereby incorporated byreference.

Different lots of oil extracted from biomass of Strain D were refined,bleached, and deodorized using standard vegetable oil processingmethods. These procedures generated oil samples RBD437, RBD469, RBD501,RBD 502, RBD503, and RBD529, which were subjected to analytical testingprotocols according to methods defined through the American OilChemists' Society, the American Society for Testing and Materials, andthe International Organization for Standardization. The results of theseanalyses are summarized below in Tables 9-14.

TABLE 9 Analytical results for oil sample RBD469. Method Number TestDescription Results Units AOCS Ca 3a-46 Insoluble impurities <0.01 %AOCS Ca 5a-40 Free Fatty Acids (Oleic) 0.02 % AOCS Ca 5a-40 Acid Value0.04 mg KOH/g AOCS CA 9f-57 Neutral oil 98.9 % D97 Cloud Point −15 degC. D97 Pour Point −18 deg C. Karl Fischer Moisture 0.01 % AOCS Cc 13d-55Chlorophyll <0.01 ppm (modified) Iodine Value 78.3 g I₂/100 g AOCS Cd8b-90 Peroxide Value 0.31 meq/kg ISO 6885 p-Anisidine Value 0.65 AOCS Cc18-80 Dropping Melting point 6.2 deg C. (Mettler) AOCS Cd 11d-96Tricylglicerides 98.6 % AOCS Cd 11d-96 Monoglyceride <0.01 % AOCS Cd11d-96 Diglycerides 0.68 % AOCS Cd 20-91 Total Polar Compounds 2.62 %IUPAC, 2.507 and Oxidized & Polymerized 17.62 % 2.508 TriacylglyceridesAOCS Cc 9b-55 Flash Point 244 deg C. AOCS Cc 9a-48 Smoke Point 232 degC. AOCS Cd 12b-92 Oxidataive Stability Index 31.6 hours Rancimat (110°C.) AOCS Ca 6a-40 Unsaponified Matter 2.28 %

RBD469 oil was analyzed for trace element content, solid fat content,and Lovibond color according to AOCS methods. Results of these analysesare presented below in Table 10, Table 10, and Table 11.

TABLE 10 ICP Elemental Analysis of RBD469 oil. Method Number TestDescription Results in ppm AOCS Ca 20-99 and Phosphorus 1.09 AOCS Ca17-01 Calcium 0.1 (modified) Magnesium 0.04 Iron <0.02 Sulfur 28.8Copper <0.05 Potassium <0.50 Sodium <0.50 Silicon 0.51 Boron 0.06Aluminum <0.20 Lead <0.20 Lithium <0.02 Nickel <0.20 Vanadium <0.05 Zinc<0.02 Arsenic <0.20 Mercury <0.20 Cadmium <0.03 Chromium <0.02 Manganese<0.05 Silver <0.05 Titanium <0.05 Selenium <0.50 UOP779 Chloride organic<1 UOP779 Chloride inorganic 7.24 AOCS Ba 4e-93 Nitrogen 6.7

TABLE 11 Solid Fat Content of RBD469 Oil Method Number Solid Fat ContentResult AOCS Cd 12b-93 Solid Fat Content 10° C. 0.13% AOCS Cd 12b-93Solid Fat Content 15° C. 0.13% AOCS Cd 12b-93 Solid Fat Content 20° C.0.28% AOCS Cd 12b-93 Solid Fat Content 25° C. 0.14% AOCS Cd 12b-93 SolidFat Content 30° C. 0.08% AOCS Cd 12b-93 Solid Fat Content 35° C. 0.25%

TABLE 12 Lovibond Color of RBD469 Oil Method Number Color Result UnitAOCS Cc 13j-97 red 2 Unit AOCS Cc 13j-97 yellow 27 Unit

RBD469 oil was subjected to transesterification to produce fatty acidmethyl esters (FAMEs). The resulting FAME profile of RBD469 is shown inTable 12.

TABLE 13 FAME Profile of RBD469 Oil Fatty Acid Area % C10 0.01 C12:00.04 C14:0 0.64 C15:0 0.08 C16:0 8.17 C16:1 iso 0.39 C16:1 0.77 C17:00.08 C18:0 1.93 C18:1 85.88 C18:1 iso 0.05 C18:2 0.05 C20:0 0.3 C20:10.06 C20:1 0.44 C22:0 0.11 C23:0 0.03 C24:0 0.1 Total FAMEs Identified99.13

The oil stability indexes (OSI) of 6 RBD oil samples withoutsupplemented antioxidants and 3 RBD oil samples supplemented withantioxidants were analyzed according to the Oil Stability Index AOCSMethod Cd 12b-92. Shown in Table 14 are the results of OSI AOCS Cd12b-92 tests, conducted at 110° C., performed using a Metrohm 873Biodiesel Rancimat. Results, except where indicated with an asterisks(*), are the average of multiple OSI runs. Those samples not analyzedare indicated (NA).

TABLE 14 Oil Stability Index at 110° C. of RBD oil samples with andwithout antioxidants. Antioxidant Antioxidant OSI (hours) for each RBDSample added Concentration RBD437 RBD469 RBD502 RBD501 RBD503 RBD529None 0    65.41   38.33 72.10 50.32 63.04 26.68 Tocopherol & 35 ppm/   77.72   48.60 82.67 NA NA NA Ascorbyl 16.7 ppm Palmitate Tocopherol &140 ppm/   130.27    81.54* 211.49* NA NA NA Ascorbyl 66.7 ppm PalmitateTocopherol & 1050 ppm/ >157*   >144     242.5* NA NA NA Ascorbyl 500 ppmPalmitate Tocopherol 50 ppm NA   46.97 NA NA NA NA TBHQ 20 ppm    63.37  37.4  NA NA NA NA

The untransformed P. moriformis (UTEX 1435) acid profile comprises lessthan 60% C18:1 fatty acids and greater than 7% C18:2 fatty acids. Incontrast, Strain D (comprising pSZ1500) exhibited fatty acid profileswith an increased composition of C18:1 fatty acids (to above 85%) and adecrease in C18:2 fatty acids (to less than 0.06%). Upon refining,bleaching, and degumming, RBD oils samples prepared from the oil madefrom strain E exhibited OSI values >26 hrs. With addition ofantioxidants, the OSI of RBD oils prepared from oils of Strain Dincreased from 48.60 hours to greater than 242 hours. In otherexperiments, OSI values of over 400 hours were achieved. Additionalproperties of a low polyunsaturated oil according to embodiments of theinvention are given in FIG. 16.

Example 6 Improving the Levels of Oleic Acid of Engineered MicrobesThrough Allelic Disruption of a Fatty Acid Desaturase and an Acyl-ACPThioesterase

This example describes the use of a transformation vector to disrupt aFATA locus of a Prototheca moriformis strain previously engineered forhigh oleic acid and low linoleic acid production. The transformationcassette used in this example comprised a selectable marker andnucleotide sequences encoding a P. moriformis KASII enzyme to engineermicroorganisms in which the fatty acid profile of the transformedmicroorganism has been altered for further increased oleic acid andlowered palmitic acid levels.

Strain D, described in Example 5 and in PCT/US2012/023696, is aclassically mutagenized (for higher oil production) derivative of P.moriformis (UTEX 1435) subsequently transformed with the transformationconstruct pSZ1500 (SEQ ID NO: 17) according to biolistic transformationmethods as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696. This strainwas used as the host for transformation with construct pSZ2276 toincrease expression of a KASII enzyme while concomitantly ablating anendogenous acyl-ACP thioesterase genetic locus to generate Strain E. ThepSZ2276 transformation construct included 5′ (SEQ ID NO: 20) and 3′ (SEQID NO: 21) homologous recombination targeting sequences (flanking theconstruct) to the FATA1 genomic region for integration into the P.moriformis nuclear genome, an A. thaliana THIC protein coding regionunder the control of the C. protothecoides actin promoter/5′UTR (SEQ IDNO: 22) and C. vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). ThisAtTHIC expression cassette is listed as SEQ ID NO: 23 and served as aselection marker. The P. moriformis KASII protein coding region wasunder the control of the P. moriformis Amt03 promoter/5′UTR (SEQ ID NO:8) and C. vulgaris nitrate reductase 3′UTR, and the native transitpeptide of the KASII enzyme was replaced with the C. protothecoidesstearoyl-ACP desaturase transit peptide (SEQ ID NO: 9). Thecodon-optimized sequence of PmKASII (Prototheca moriformis KASII)comprising a C. protothecoides S106 stearoyl-ACP desaturase transitpeptide is provided the sequence listings as SEQ ID NO: 24. SEQ ID NO:25 provides the protein translation of SEQ ID NO: 24. The protein codingregions of PmKASII and suc2 were codon optimized to reflect the codonbias inherent in P. moriformis UTEX 1435 nuclear genes as described inPCT/U52009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

Primary pSZ2276 transformants of Strain D were selected on agar plateslacking thiamine, clonally purified, and a single engineered line,strain E was selected for analysis. Strain E was cultivated underheterotrophic lipid production conditions at pH5.0 and pH7.0 asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples were preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples were analyzed using standard fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1. The fatty acid profiles (expressed as Area % oftotal fatty acids) from the transgenic line arising from transformationwith pSZ2276 into Strain D are shown in Table 15.

TABLE 15 Fatty acid profiles of Prototheca moriformis (UTEX 1435)Strains A, D, and E engineered for increased oleic acid and loweredlinoleic acid levels. Transformation Area % Fatty Acid StrainConstruct(s) pH C16:0 C18:0 C18:1 C18:2 C20:1 Strain None pH 5 26.6 3.360.5 6.7 0.07 A Strain None pH 7 28.3 4.1 58 6.5 0.06 A Strain pSZ1500pH 5 17 3.6 77.1 0.01 0.14 D Strain pSZ1500 pH 7 19.5 5.3 72.6 0.01 0.09D Strain pSZ1500 + pH 5 4.1 2.36 88.5 0.04 3.1 E pSZ2276 StrainpSZ1500 + pH 7 2.1 7.8 87.9 0.01 0.5 E pSZ2276

As shown in Table 15, targeted interruption of FADc alleles with a CtOTEexpression cassette impacted the fatty acid profiles of transformedmicroorganisms. Fatty acid profiles of Strain D (comprising the pSZ1500transformation vector) showed increased composition of C18:1 fatty acidswith a concomitant decrease in C16:0 and C18:2 fatty acids relative toStrain A. Subsequent transformation of Strain D with pSZ2276 tooverexpress a P. moriformis (UTEX 1435) KASII protein whileconcomitantly ablating a FATA genetic locus (thereby generating StrainE) resulted in still further impact on the fatty acid profiles of thetransformed microorganisms. Fatty acid profiles of Strain E showedincreased composition of C18:1 fatty acids, with a further decrease inC16:0 fatty acids relative to Strains A and D. Propagation of Strain Ein culture conditions at pH 7, to induce expression from the Amt03promoter, resulted in a fatty acid profile that was higher in C18:0 andC18:1 fatty acids and lower in C16:0 fatty acids, relative to the samestrain cultured at pH 5.

These data demonstrate the utility of multiple genetic modifications toimpact the fatty acid profile of a host organism for increased levels ofoleic acid with concomitant decreased levels of linoleic acid andpalmitic acid. Further, this example illustrates the use of recombinantpolynucleotides to target gene interruption of an endogenous FATA allelewith a cassette comprising a pH-regulatable promoter to controlexpression of an exogenous KASII protein-coding region in order to alterthe fatty acid profile of a host microbe.

Example 7 Conditional Expression of a Fatty Acid Desaturase

This example describes the use of a transformation vector toconditionally express a delta 12 fatty acid desaturase (FADs) in aPrototheca moriformis strain previously engineered for high oleic acidand very low linoleic acid production in both seed and lipidproductivity stages of propagation. Very low linoleic acid levels incell oils are sought for use in certain applications. However, absenceof linoleic acid during cell division phase (“seed stage”) of a hostmicrobe is disadvantageous. Linoleic acid may be supplemented to theseed medium to hasten cell division and not added during lipidproduction, but this addition imposes unwanted costs. To overcome thischallenge, a transformation cassette was constructed for regulatedexpression of a FAD2 enzyme such that levels of linoleic acidssufficient for cell division could be achieved and oil with very lowlevels of linoleic acids could be produced during the oil productionphase of culture of a microorganism. The transformation cassette used inthis example comprised a selectable marker, a pH-regulatable promoter,and nucleotide sequences encoding a P. moriformis FAD2 enzyme toengineer microorganisms in which the fatty acid profile of thetransformed microorganism has been altered for increased oleic acidproduction and regulatable linoleic acid production.

Strain D, described in Examples 5, 6, and in PCT/US2012/023696, is aclassically mutagenized (for higher oil production) derivative of P.moriformis (UTEX 1435) subsequently transformed with the transformationconstruct pSZ1500 (SEQ ID NO: 17) according to biolistic transformationmethods as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696. This strainwas used as the host for transformation with construct pSZ2413 tointroduce a pH-driven promoter for regulation of a P. moriformis FAD2enzyme. The pSZ2413 transformation construct included 5′ (SEQ ID NO: 1)and 3′ (SEQ ID NO: 2) homologous recombination targeting sequences(flanking the construct) to the 6S genomic region for integration intothe P. moriformis nuclear genome, an A. thaliana THIC protein codingregion under the control of the C. protothecoides actin promoter/5′UTR(SEQ ID NO: 22) and C. vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6).This AtTHIC expression cassette is listed as SEQ ID NO: 23 and served asa selection marker. The P. moriformis FAD2 protein coding region wasunder the control of the P. moriformis Amt03 promoter/5′UTR (SEQ ID NO:8) and C. vulgaris nitrate reductase 3′UTR. The codon-optimized sequenceof PmFAD2 is provided the sequence listings as SEQ ID NO: 26. SEQ ID NO:27 provides the protein translation of SEQ ID NO: 26. The protein codingregions of PmFAD2 and suc2 were codon optimized to reflect the codonbias inherent in P. moriformis UTEX 1435 nuclear genes as described inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

Primary pSZ2413 transformants of Strain D were selected on agar plateslacking thiamine, clonally purified, and isolates of the engineeredline, Strain F were selected for analysis. These isolates werecultivated under heterotrophic lipid production conditions at pH7.0 (toactivate expression of FAD2 from the PmAmt03 promoter) and at pH5.0, asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples were preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples were analyzed using standard fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1. The resulting profile of C18:2 fatty acids(expressed in Area %) from nine representative isolates of transgenicStrain F (F-1 through F-9) arising from transformation with pSZ2413 intoStrain D are shown in Table 16.

TABLE 16 C18:2 fatty acid profiles of Prototheca moriformis (UTEX 1435)Strains A, D, and F. Area % C18:2 Strain Transformation Construct (s) pH5.0 pH 7.0 A None 6.07 7.26 D pSZ1500 0.01 0.01 F-1 pSZ1500 + pSZ24130.37 5.29 F-2 pSZ1500 + pSZ2413 0.45 6.87 F-3 pSZ1500 + pSZ2413 0.506.79 F-4 pSZ1500 + pSZ2413 0.57 5.06 F-5 pSZ1500 + pSZ2413 0.57 7.58 F-6pSZ1500 + pSZ2413 0.60 6.88 F-7 pSZ1500 + pSZ2413 0.62 6.52 F-8pSZ1500 + pSZ2413 0.63 5.79 F-9 pSZ1500 + pSZ2413 0.77 4.53

As shown in Table 16 the impact of regulated expression of the PmFAD2enzyme, effected though strain culture at different pH levels, is aclear increase in the composition of C18:2 fatty acids in thetransformed microorganism. Linoleic acid comprises about 6% to about7.3% of fatty acids of Strain A. In contrast, Strain D (comprising thepSZ1500 transformation vector to ablate both FAD2 alleles) ischaracterized by a fatty acid profile of 0.01% linoleic acid.Transformation of Strain D with pSZ2413 to generate Strain F results ina recombinant microbe in which the production of linoleic acid isregulated by the Amt03 promoter. Propagation of Strain F isolates inculture conditions at pH 7, to induce FAD2 expression from the Amt03promoter, resulted in a fatty acid profile characterized by about 4.5%to about 7.5% linoleic acid. In contrast, propagation of Strain Fisolates in culture conditions at pH 5 resulted in a fatty acid profilecharacterized by about 0.33 to about 0.77% linoleic acid.

These data demonstrate the utility of and effectiveness of recombinantpolynucleotides permitting conditional expression of a FAD2 enzyme toalter the fatty acid profile of engineered microorganisms, and inparticular in regulating the production of C18:2 fatty acids inmicrobial cells.

Example 8 Analysis of Regiospecific Profile

LC/MS TAG distribution analyses were carried out using a Shimadzu Nexeraultra high performance liquid chromatography system that included aSIL-30AC autosampler, two LC-30AD pumps, a DGU-20A5 in-line degasser,and a CTO-20A column oven, coupled to a Shimadzu LCMS 8030 triplequadrupole mass spectrometer equipped with an APCI source. Data wasacquired using a Q3 scan of m/z 350-1050 at a scan speed of 1428 u/secin positive ion mode with the CID gas (argon) pressure set to 230 kPa.The APCI, desolvation line, and heat block temperatures were set to 300,250, and 200° C., respectively, the flow rates of the nebulizing anddrying gases were 3.0 L/min and 5.0 L/min, respectively, and theinterface voltage was 4500 V. Oil samples were dissolved indichloromethane-methanol (1:1) to a concentration of 5 mg/mL, and 0.8 μLof sample was injected onto Shimadzu Shim-pack XR-ODS III (2.2 μm,2.0×200 mm) maintained at 30° C. A linear gradient from 30%dichloromethane-2-propanol (1:1)/acetonitrile to 51%dichloromethane-2-propanol (1:1)/acetonitrile over 27 minutes at 0.48mL/min was used for chromatographic separations.

Example 9 Engineering Microbes for Increased Production of SOS, POP, AndPOS Triacylglycerides

This example describes the use of recombinant polynucleotides thatencode a C18:0-preferring Brassica napus thioesterase (BnOTE) enzyme toengineer a microorganism in which the triacylglyceride distribution ofthe transformed microorganism has been enriched in SOS, POS, and POPtriacylglycerides.

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain A, was initially transformed with the plasmid construct pSZ1358according to biolistic transformation methods as described inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. pSZ1358, described inPCT/US2012/023696, hereby incorporated by reference, comprised thecoding sequence of the Brassica napus thioesterase (BnOTE) thioesterase(SEQ ID NO: 28), 5′ (SEQ ID NO: 1) and 3′ (SEQ ID NO: 2) homologousrecombination targeting sequences (flanking the construct) to the 6Sgenomic region for integration into the nuclear genome, and a S.cerevisiae suc2 sucrose invertase coding region (SEQ ID NO: 4), toexpress the protein sequence given in SEQ ID NO: 3, under the control ofC. reinhardtii β-tubulin promoter/5′UTR (SEQ ID NO: 5) and Chlorellavulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). This S. cerevisiaesuc2 expression cassette is listed as SEQ ID NO: 7 and served as aselectable marker. The BnOTE protein coding sequence to express theprotein sequence given in SEQ ID NO: 29, was under the control of the P.moriformis Amt03 promoter/5′UTR (SEQ ID NO: 8) and C. vulgaris nitratereductase 3′UTR. The protein coding regions of BnOTE and suc2 were codonoptimized to reflect the codon bias inherent in P. moriformis UTEX 1435nuclear genes as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696.

Primary pSZ1358 transformants of Strain A were selected on agar platescontaining sucrose as a sole carbon source, clonally purified, andsingle engineered line, Strain G was selected for analysis. Strain G wascultivated under heterotrophic lipid production conditions at pH7.0 (toactivate expression of BnOTE from the PmAmt03 promoter) as described inPCT/U52009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Oil samples obtained fromStrain A and Strain G were analyzed for fatty acid composition usingmethods described in Examples 1 and 2, and, using the methods describedin Example 8, for the regiospecificity of triacylglycerides in the oil.Fatty acid profiles of TAGs isolated from Strain A and G are shown inTable 17. Table 18 presents the regiospecificity profile of POP, POS,and SOS TAGs present in oil samples from Strain A and G.

TABLE 17 Effect of BnOTE expression on the fatty acid composition andthe sn-2 profile of TAGs produced from transformed Protothecamoriformis. Strain G Area % Strain A (pSZ1358) Fatty acid FA profile FAprofile C10:0 n.r. 0.5 C12:0 n.r. 0.5 C14:0 1.0 1.3 C16:0 23.9 25.8C18:0 3.7 30.4 C18:1 64.3 30.2 C18:2 4.5 8.8 C18:3 α n.r. 0.4

TABLE 18 Effect of BnOTE expression on the regiospecific profile of POP,POS, and SOS TAGs produced from transformed Prototheca moriformis.Strain A (untransformed) Strain G (pSZ1358) Cocoa Butter Area NormalizedArea Normalized Area Normalized TAG % Area % % Area % % Area % POP 13.0976.8 10.6 23.5 17.9 22.1 POS 3.51 20.5 21.0 46.6 39.2 48.4 SOS 0.45 2.613.5 29.9 23.9 29.5 total 17.05 100 45.0 100 81.1 100

As shown in Table 17, the fatty acid composition of TAGs isolated fromStrain G expressing BnOTE was markedly increased for C18:0 fatty acids(from 3.7% to 30.4%) and decreased in C18:1 fatty acids (from 64.3% to30.2%) relative to the fatty acid profile of TAGs isolated fromuntransformed Strain A. The fatty acid composition of TAGs isolated fromStrain A was characterized by about 23.9% palmitic acid, 3.7% stearicacid, and 64.3% oleic acid, a ratio for P:S:O of about 6.5:1:17.4. Incontrast, the fatty acid composition of TAGs isolated from Strain G wascharacterized by about 25.8% palmitic acid, 30.4% stearic acid, and30.2% oleic acid, a ratio for P:O:S of about 1:1.18:1.17.

The impact of expression of a C18:0 preferring thioesterase on theregiospecific profile of POP, POS, and SOS TAGs of oils produced fromthe transformed microorganism was an increase in all three TAGs as aproportion of the total TAGs present in the oil. As shown in Table 18,the sum of POP+POS+SOS TAGs accounted for 45% of the TAGs produced byStrain G, whereas POP, POS, and SOS TAGs summed to only about 17% ofTAGs produced in Strain A. The percentages of POP, POS and SOS of strainG are compared to Cocoa butter in Table 18. As can be seen, ratios ofPOP, POS and SOS of Strain G are very similar to the ratios observed incocoa butter.

These data demonstrate the utility and effectiveness of polynucleotidespermitting exogenous thioesterase expression to alter the fatty acid andregiospecific profiles of TAGs of engineered microorganisms, inparticular to increase the distribution of POP, POS, and SOS TAGs.

Examples 10-33 Engineering of Microorganisms

Examples 10-33 below describe the engineering of various microorganismsin accordance with the present invention. To alter the fatty acidprofile of a microorganism, microorganisms can be genetically modifiedwherein endogenous or exogenous lipid biosynthesis pathway enzymes areexpressed, overexpressed, or attenuated. Steps to genetically engineer amicrobe to alter its fatty acid profile as to the degree of fatty acidunsaturation and to decrease or increase fatty acid chain lengthcomprise the design and construction of a transformation vector (e.g., aplasmid), transformation of the microbe with one or more vectors,selection of transformed microbes (transformants), growth of thetransformed microbe, and analysis of the fatty acid profile of thelipids produced by the engineered microbe.

Transgenes that alter the fatty acid profiles of host organisms can beexpressed in numerous eukaryotic microbes. Examples of expression oftransgenes in eukaryotic microbes including Chlamydomonas reinhardtii,Chlorella elhpsoidea, Chlorella saccarophila, Chlorella vulgaris,Chlorella kessleri, Chlorella sorokiniana, Haematococcus pluvialis,Gonium pectorals, Volvox carteri, Dunaliella tertiolecta, Dunaliellaviridis, Dunaliella salina, Closterium peracerosum-strigosum-littoralecomplex, Nannochloropsis sp., Thalassiosira pseudonana, Phaeodactylumtricornutum, Navicula saprophila, Cylindrotheca fusiformis, Cyclotellacryptica, Symbiodinium microadriacticum, Amphidinium sp., Chaetocerossp., Mortierella alpina, and Yarrowia hpolytica can be found in thescientific literature. These expression techniques can be combined withthe teachings of the present invention to produce engineeredmicroorganisms with altered fatty acid profiles.

Transgenes that alter the fatty acid profiles of host organisms or alterthe regiospecific distribution of glycerolipids produced by hostorganisms can also be expressed in numerous prokaryotic microbes.Examples of expression of transgenes in oleaginous microbes includingRhodococcus opacus can be found in the literature. These expressiontechniques can be combined with the teachings of the present inventionto produce engineered microorganisms with altered fatty acid profiles.

TABLES 19A-D Codon preference listing. Haemato Amino Chlorella ChlorellaChlorella Chlorella Dunaliella Volvox coccus Acid Codon sorokinianavulgaris ellipsoidea kessleri tertiolecta carteri pluvialis Ala GCG 0.200.25 0.15 0.14 0.09 0.25 0.21 Ala GCA 0.05 0.24 0.32 0.10 0.17 0.13 0.27Ala GCT 0.12 0.16 0.26 0.18 0.31 0.26 0.17 Ala GCC 0.63 0.35 0.27 0.580.43 0.36 0.35 Arg AGG 0.03 0.09 0.10 0.09 0.26 0.08 0.14 Arg AGA 0.040.05 0.14 0.01 0.09 0.03 0.05 Arg CGG 0.06 0.19 0.09 0.06 0.06 0.17 0.15Arg CGA 0.00 0.10 0.08 0.00 0.08 0.08 0.10 Arg CGT 0.06 0.09 0.37 0.140.12 0.22 0.13 Arg CGC 0.81 0.48 0.22 0.71 0.40 0.43 0.42 Asn AAT 0.040.16 0.43 0.06 0.27 0.23 0.21 Asn AAC 0.96 0.84 0.57 0.94 0.73 0.77 0.79Asp GAT 0.13 0.25 0.47 0.12 0.40 0.35 0.27 Asp GAC 0.87 0.75 0.53 0.880.60 0.65 0.73 Cys TGT 0.06 0.13 0.43 0.09 0.20 0.17 0.27 Cys TGC 0.940.87 0.57 0.91 0.80 0.83 0.64 End TGA 0.00 0.72 0.14 0.14 0.36 0.24 0.70End TAG 0.33 0.11 0.29 0.00 0.00 0.18 0.22 End TAA 0.67 0.17 4.00 0.860.64 0.59 0.09 Gln CAG 0.42 0.40 0.15 0.40 0.27 0.29 0.33 Gln CAA 0.040.04 0.21 0.40 0.27 0.07 0.10 Glu GAG 0.53 0.50 0.33 0.40 0.27 0.53 0.49Glu GAA 0.02 0.06 0.31 0.40 0.27 0.11 0.07 Gly GGG 0.04 0.16 0.19 0.080.10 0.12 0.22 Gly GGA 0.02 0.11 0.13 0.07 0.13 0.12 0.11 Gly GGT 0.030.12 0.39 0.24 0.25 0.23 0.15 Gly GGC 0.91 0.61 0.29 0.96 0.51 0.53 0.52His CAT 0.14 0.16 0.30 0.08 0.25 0.35 0.27 His CAC 0.86 0.84 0.70 0.930.75 0.65 0.73 Ile ATA 0.00 0.04 0.07 0.01 0.04 0.08 0.09 Ile ATT 0.150.30 0.63 0.29 0.31 0.35 0.29 Ile ATC 0.85 0.66 0.65 0.69 0.65 0.57 0.62Leu TTG 0.03 0.07 0.03 0.05 0.14 0.14 0.16 Leu TTA 0.00 0.01 0.32 0.000.02 0.03 0.02 Leu CTG 0.72 0.61 0.34 0.61 0.60 0.45 0.53 Leu CTA 0.010.03 0.03 0.04 0.04 0.07 0.07 Leu CTT 0.04 0.08 0.16 0.06 0.06 0.14 0.09Leu CTC 0.20 0.20 0.12 0.24 0.14 0.17 0.13 Lys AAG 0.98 0.94 0.54 0.980.90 0.90 0.84 Lys AAA 0.02 0.06 0.46 0.02 0.10 0.10 0.16 Met ATG 1.001.00 1.00 1.00 1.00 1.00 1.00 Phe TTT 0.28 0.32 0.42 0.31 0.24 0.27 0.35Phe TTC 0.72 0.68 0.58 0.69 0.76 0.73 0.65 Pro CCG 0.18 0.31 0.09 0.070.04 0.34 0.15 Pro CCA 0.06 0.17 0.36 0.07 0.04 0.20 0.24 Pro CCT 0.100.14 0.25 0.17 0.04 0.19 0.29 Pro CCC 0.66 0.38 0.29 0.69 0.04 0.27 0.32Ser AGT 0.03 0.04 0.14 0.02 0.08 0.08 0.07 Ser AGC 0.27 0.38 0.18 0.180.31 0.27 0.31 Ser TCG 0.12 0.14 0.08 0.10 0.02 0.19 0.10 Ser TCA 0.030.08 0.14 0.08 0.09 0.09 0.14 Ser TCT 0.09 0.11 0.26 0.18 0.19 0.14 0.13Ser TCC 0.47 0.24 0.20 0.44 0.30 0.24 0.24 Thr ACG 0.11 0.20 0.13 0.050.12 0.27 0.19 Thr ACA 0.01 0.20 0.32 0.07 0.20 0.12 0.23 Thr ACT 0.120.13 0.29 0.12 0.24 0.20 0.18 Thr ACC 0.76 0.47 0.26 0.76 0.44 0.41 0.40Trp TGG 1.00 1.00 1.00 1.00 1.00 1.00 1.00 Tyr TAT 0.07 0.15 0.43 0.270.28 0.24 0.19 Tyr TAC 0.93 0.85 0.57 0.73 0.72 0.76 0.81 Val GTG 0.710.54 0.37 0.60 0.54 0.46 0.62 Val GTA 0.00 0.05 0.25 0.03 0.09 0.07 0.09Val GTT 0.11 0.14 0.24 0.09 0.14 0.17 0.09 Val GTC 0.18 0.27 0.14 0.280.23 0.30 0.21 Closterium peracerosum- strigosum- Amino littoraleDunaliella Dunaliella Gonium Phaeodactylum Chaetoceros Acid Codoncomplex viridis sauna pectorale tricornutum cornpressum Ala GCG 0.480.13 0.15 0.43 0.15 0.08 Ala GCA 0.10 0.27 0.20 0.09 0.10 0.37 Ala GCT0.15 0.25 0.27 0.08 0.23 0.36 Ala GCC 0.26 0.35 0.39 0.41 0.52 0.18 ArgAGG 0.04 0.25 0.22 0.13 0.02 0.14 Arg AGA 0.00 0.06 0.05 0.00 0.04 0.29Arg CGG 0.18 0.08 0.12 0.40 0.10 0.00 Arg CGA 0.00 0.06 0.06 0.05 0.120.19 Arg CGT 0.13 0.15 0.13 0.08 0.41 0.38 Arg CGC 0.64 0.39 0.43 0.350.31 0.00 Asn AAT 0.04 0.17 0.23 0.07 0.30 0.58 Asn AAC 0.96 0.83 0.770.93 0.65 0.42 Asp GAT 0.30 0.38 0.40 0.11 0.41 0.53 Asp GAC 0.70 0.620.60 0.89 0.59 0.47 Cys TGT 0.06 0.24 0.17 0.20 0.39 0.44 Cys TGC 0.940.76 0.83 0.90 0.61 0.56 End TGA 0.75 0.31 0.37 0.50 0.06 0.50 End TAG0.00 0.15 0.14 0.00 0.13 0.00 End TAA 0.25 0.54 0.49 0.50 0.81 0.50 GlnCAG 0.53 0.36 0.32 0.31 0.23 0.16 Gln CAA 0.09 0.12 0.08 0.07 0.14 0.19Glu GAG 0.31 0.44 0.51 0.56 0.21 0.28 Glu GAA 0.06 0.09 0.09 0.07 0.420.37 Gly GGG 0.31 0.14 0.10 0.18 0.08 0.12 Gly GGA 0.06 0.11 0.12 0.090.34 0.33 Gly GGT 0.09 0.22 0.22 0.07 0.30 0.39 Gly GGC 0.53 0.54 0.560.65 0.28 0.16 His CAT 0.33 0.25 0.25 0.43 0.28 0.84 His CAC 0.67 0.750.75 0.57 0.72 0.16 Ile ATA 0.03 0.03 0.03 0.07 0.03 0.12 Ile ATT 0.230.25 0.31 0.33 0.51 0.65 Ile ATC 0.74 0.72 0.66 0.59 0.46 0.23 Leu TTG0.04 0.11 0.12 0.04 0.26 0.11 Leu TTA 0.00 0.01 0.01 0.00 0.02 0.14 LeuCTG 0.31 0.60 0.61 0.64 0.15 0.05 Leu CTA 0.01 0.05 0.04 0.01 0.05 0.08Leu CTT 0.04 0.07 0.08 0.05 0.18 0.51 Leu CTC 0.60 0.16 0.14 0.26 0.340.11 Lys AAG 0.86 0.87 0.89 0.93 0.75 0.52 Lys AAA 0.14 0.13 0.11 0.070.25 0.48 Met ATG 1.00 1.00 1.00 1.00 1.00 1.00 Phe TTT 0.09 0.25 0.290.10 0.44 0.65 Phe TTC 0.91 0.75 0.71 0.90 0.56 0.35 Pro CCG 0.28 0.100.08 0.53 0.29 0.05 Pro CCA 0.15 0.10 0.17 0.09 0.12 0.45 Pro CCT 0.120.10 0.30 0.04 0.20 0.33 Pro CCC 0.44 0.10 0.45 0.34 0.40 0.17 Ser AGT0.04 0.09 0.06 0.02 0.12 0.14 Ser AGC 0.05 0.31 0.32 0.20 0.12 0.07 SerTCG 0.22 0.04 0.06 0.42 0.19 0.08 Ser TCA 0.16 0.08 0.10 0.09 0.06 0.31Ser TCT 0.05 0.17 0.15 0.07 0.15 0.23 Ser TCC 0.47 0.31 0.30 0.20 0.350.18 Thr ACG 0.30 0.16 0.13 0.42 0.23 0.10 Thr ACA 0.06 0.21 0.18 0.030.13 0.38 Thr ACT 0.22 0.18 0.23 0.08 0.19 0.27 Thr ACC 0.42 0.46 0.460.47 0.45 0.25 Trp TGG 1.00 1.00 1.00 1.00 1.00 1.00 Tyr TAT 0.07 0.160.21 0.12 0.18 0.67 Tyr TAC 0.93 0.84 0.79 0.88 0.82 0.33 Val GTG 0.500.64 0.62 0.57 0.22 0.30 Val GTA 0.02 0.03 0.05 0.04 0.09 0.27 Val GTT0.06 0.11 0.11 0.04 0.22 0.10 Val GTC 0.42 0.22 0.23 0.35 0.47 0.33Symbio- Thal- Cylindro- Amphi- dinium Nanno- assiosira Amino thecadinium micro- chloro- Cyclotella Nayicula pseudo- C. Acid Codonfusiformis carterae adriacticum psis sp cryptica pelliculosa nanareinhardtii Ala GCG 0.07 0.17 0.22 0.24 0.11 0.00 0.11 0.35 Ala GCA 0.140.33 0.26 0.10 0.16 0.13 0.25 0.08 Ala GCT 0.35 0.29 0.20 0.17 0.45 0.440.33 0.13 Ala GCC 0.43 0.20 0.32 0.48 0.27 0.44 0.30 0.43 Arg AGG 0.090.15 0.27 0.00 0.09 0.05 0.18 0.05 Arg AGA 0.14 0.03 0.27 0.00 0.05 0.100.17 0.01 Arg CGG 0.06 0.08 0.09 0.00 0.04 0.05 0.06 0.20 Arg CGA 0.160.18 0.09 0.29 0.08 0.35 0.11 0.04 Arg CGT 0.34 0.18 0.09 0.14 0.47 0.200.34 0.09 Arg CGC 0.22 0.40 0.18 0.57 0.28 0.25 0.15 0.62 Asn AAT 0.420.37 0.21 0.00 0.25 0.47 0.43 0.09 Asn AAC 0.58 0.63 0.79 1.00 0.75 0.530.57 0.91 Asp GAT 0.54 0.54 0.50 0.20 0.52 0.20 0.56 0.14 Asp GAC 0.460.46 0.50 0.80 0.48 0.80 0.44 0.86 Cys TGT 0.44 0.75 0.50 0.00 0.29 0.100.54 0.10 Cys TGC 0.56 0.25 0.50 1.00 0.71 0.90 0.46 0.90 End TGA 0.130.50 1.00 0.00 0.10 0.00 0.31 0.27 End TAG 0.10 0.00 0.00 0.00 0.00 0.000.38 0.22 End TAA 0.77 0.50 0.00 1.00 0.90 1.00 0.31 0.52 Gln CAG 0.120.33 0.28 0.41 0.19 0.21 0.16 0.38 Gln CAA 0.25 0.15 0.17 0.00 0.17 0.280.19 0.04 Glu GAG 0.23 0.41 0.50 0.59 0.38 0.17 0.40 0.55 Glu GAA 0.390.10 0.06 0.00 0.26 0.34 0.26 0.03 Gly GGG 0.06 0.19 0.32 0.10 0.10 0.030.12 0.11 Gly GGA 0.47 0.10 0.12 0.05 0.45 0.28 0.51 0.06 Gly GGT 0.350.34 0.16 0.25 0.22 0.13 0.23 0.11 Gly GGC 0.12 0.37 0.40 0.60 0.24 0.560.14 0.72 His CAT 0.39 0.12 0.40 0.00 0.42 1.00 0.50 0.11 His CAC 0.610.88 0.60 1.00 0.58 0.00 0.50 0.89 Ile ATA 0.06 0.05 0.00 0.00 0.04 0.000.08 0.03 Ile ATT 0.42 0.53 0.38 0.14 0.53 0.73 0.38 0.22 Ile ATC 0.520.42 0.63 0.86 0.42 0.27 0.54 0.75 Leu TTG 0.26 0.35 0.39 0.22 0.20 0.160.29 0.04 Leu TTA 0.09 0.01 0.00 0.00 0.03 0.00 0.05 0.01 Leu CTG 0.090.22 0.39 0.09 0.06 0.12 0.08 0.73 Leu CTA 0.05 0.00 0.04 0.00 0.03 0.040.06 0.03 Leu CTT 0.37 0.31 0.13 0.04 0.39 0.36 0.20 0.05 Leu CTC 0.130.12 0.04 0.65 0.29 0.32 0.32 0.15 Lys AAG 0.60 0.93 0.85 1.00 0.70 0.830.76 0.95 Lys AAA 0.40 0.07 0.15 0.00 0.30 0.17 0.24 0.05 Met ATG 1.001.00 1.00 1.00 1.00 1.00 1.00 1.00 Phe TTT 0.37 0.21 0.25 0.20 0.31 0.780.38 0.16 Phe TTC 0.63 0.79 0.75 0.80 0.69 0.22 0.62 0.84 Pro CCG 0.110.14 0.18 0.08 0.10 0.21 0.16 0.33 Pro CCA 0.33 0.42 0.09 0.08 0.16 0.290.31 0.08 Pro CCT 0.32 0.22 0.41 0.25 0.35 0.21 0.31 0.13 Pro CCC 0.240.22 0.32 0.58 0.39 0.29 0.23 0.47 Ser AGT 0.12 0.13 0.09 0.00 0.09 0.130.18 0.04 Ser AGC 0.09 0.24 0.14 0.13 0.08 0.28 0.11 0.35 Ser TCG 0.130.03 0.05 0.00 0.15 0.25 0.17 0.25 Ser TCA 0.12 0.25 0.05 0.00 0.12 0.080.12 0.05 Ser TCT 0.30 0.16 0.23 0.13 0.39 0.25 0.23 0.07 Ser TCC 0.240.19 0.45 0.75 0.18 0.03 0.19 0.25 Thr ACG 0.09 0.14 0.10 0.28 0.10 0.180.21 0.30 Thr ACA 0.15 0.28 0.10 0.00 0.15 0.09 0.19 0.08 Thr ACT 0.390.12 0.10 0.17 0.33 0.41 0.28 0.10 Thr ACC 0.37 0.47 0.70 0.56 0.43 0.320.32 0.52 Trp TGG 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 Tyr TAT 0.380.32 0.20 0.00 0.38 0.20 0.39 0.10 Tyr TAC 0.62 0.68 0.80 1.00 0.62 0.800.61 0.90 Val GTG 0.11 0.65 0.67 0.31 0.16 0.18 0.29 0.67 Val GTA 0.060.05 0.00 0.00 0.09 0.09 0.16 0.03 Val GTT 0.38 0.08 0.11 0.15 0.42 0.090.28 0.07 Val GTC 0.46 0.21 0.22 0.54 0.33 0.64 0.27 0.22 Amino YarrowiaMortierella Rhodococcus Acid Codon lipolytica alpina opacus Ala GCG 0.080.14 0.35 Ala GCA 0.11 0.12 0.14 Ala GCT 0.35 0.29 0.09 Ala GCC 0.460.45 0.43 Arg AGG 0.05 0.05 0.05 Arg AGA 0.13 0.06 0.02 Arg CGG 0.120.06 0.26 Arg CGA 0.52 0.09 0.12 Arg CGT 0.11 0.32 0.11 Arg CGC 0.070.42 0.44 Asn AAT 0.17 0.15 0.21 Asn AAC 0.83 0.85 0.79 Asp GAT 0.350.42 0.24 Asp GAC 0.65 0.58 0.76 Cys TGT 0.46 0.13 0.26 Cys TGC 0.540.87 0.74 End TGA 0.16 0.05 0.72 End TAG 0.38 0.25 0.17 End TAA 0.460.70 0.11 Gln CAG 0.33 0.36 0.28 Gln CAA 0.08 0.06 0.06 Glu GAG 0.440.49 0.45 Glu GAA 0.14 0.09 0.22 Gly GGG 0.05 0.03 0.18 Gly GGA 0.280.29 0.15 Gly GGT 0.32 0.32 0.20 Gly GGC 0.34 0.36 0.48 His CAT 0.340.27 0.20 His CAC 0.66 0.73 0.80 Ile ATA 0.03 0.01 0.05 Ile ATT 0.440.33 0.14 Ile ATC 0.53 0.66 0.81 Leu TTG 0.09 0.27 0.09 Leu TTA 0.020.00 0.01 Leu CTG 0.37 0.26 0.41 Leu CTA 0.05 0.02 0.03 Leu CTT 0.180.12 0.06 Leu CTC 0.29 0.32 0.40 Lys AAG 0.84 0.91 0.80 Lys AAA 0.160.09 0.20 Met ATG 1.00 1.00 1.00 Phe TTT 0.38 0.39 0.09 Phe TTC 0.620.61 0.91 Pro CCG 0.10 0.07 0.52 Pro CCA 0.10 0.08 0.09 Pro CCT 0.320.36 0.07 Pro CCC 0.47 0.49 0.32 Ser AGT 0.07 0.05 0.08 Ser AGC 0.110.14 0.23 Ser TCG 0.16 0.32 0.33 Ser TCA 0.08 0.08 0.07 Ser TCT 0.280.12 0.05 Ser TCC 0.30 0.29 0.24 Thr ACG 0.11 0.17 0.28 Thr ACA 0.140.10 0.11 Thr ACT 0.26 0.23 0.07 Thr ACC 0.49 0.49 0.53 Trp TGG 1.001.00 1.00 Tyr TAT 0.18 0.20 0.18 Tyr TAC 0.82 0.80 0.82 Val GTG 0.330.22 0.37 Val GTA 0.05 0.02 0.05 Val GTT 0.26 0.27 0.10 Val GTC 0.360.49 0.49

TABLE 20 Lipid biosynthesis pathway proteins 3-Ketoacyl ACP synthaseCuphea hookeriana 3-ketoacyl-ACP synthase (GenBank Acc. No. AAC68861.1),Cuphea wrightii beta-ketoacyl-ACP synthase II (GenBank Acc. No.AAB37271.1), Cuphea lanceolata beta-ketoacyl-ACP synthase IV (GenBankAcc. No. CAC59946.1), Cuphea wrightii beta-ketoacyl-ACP synthase II(GenBank Acc. No. AAB37270.1), Ricinus communis ketoacyl-ACP synthase(GenBank Acc. No. XP_002516228), Gossypium hirsutum ketoacyl- ACPsynthase (GenBank Acc. No. ADK23940.1), Glycine max plastid3-keto-acyl-ACP synthase II-A (GenBank Acc No. AAW88763.1), Elaeisguineensis beta-ketoacyl-ACP synthase II (GenBank Acc. No. AAF26738.2),Helianthus annuus plastid 3-keto-acyl-ACP synthase I (GenkBank Acc. No.ABM53471.1), Glycine max3-keto-acyl-ACP synthase I (GenBank Acc. No.NP_001238610.1), Helianthus annuus plastid 3-keto-acyl-ACP synthase II(GenBank Acc ABI18155.1), Brassica napus beta-ketoacyl-ACP synthetase 2(GenBank Acc. No. AAF61739.1), Perilla frutescens beta-ketoacyl-ACPsynthase II (GenBank Acc. No. AAC04692.1), Helianthus annusbeta-ketoacyl-ACP synthase II (GenBank Accession No. ABI18155), Ricinuscommunis beta-ketoacyl-ACP synthase II (GenBank Accession No. AAA33872),Haematococcus pluvialis beta-ketoacyl acyl carrier protein synthase(GenBank Accession No. HM560033.1), Jatropha curcasbeta ketoacyl-ACPsynthase I (GenBank Accession No. ABJ90468.1), Populus trichocarpabeta-ketoacyl-ACP synthase I (GenBank Accession No. XP_002303661.1),Coriandrum sativum beta-ketoacyl-ACP synthetase I (GenBank Accession No.AAK58535.1), Arabidopsis thaliana 3-oxoacyl-[acyl-carrier- protein]synthase I (GenBank Accession No. NP_001190479.1), Vitis vinifera3-oxoacyl- [acyl-carrier-protein] synthase I (GenBank Accession No.XP_002272874.2) Fatty acyl-ACP Thioesterases Umbellularia californicafatty acyl-ACP thioesterase (GenBank Acc. No. AAC49001), Cinnamomumcamphora fatty acyl-ACP thioesterase (GenBank Acc. No. Q39473),Umbellularia californica fatty acyl-ACP thioesterase (GenBank Acc. No.Q41635), Myristica fragrans fatty acyl-ACP thioesterase (GenBank Acc.No. AAB71729), Myristica fragrans fatty acyl-ACP thioesterase (GenBankAcc. No. AAB71730), Elaeis guineensis fatty acyl- ACP thioesterase(GenBank Acc. No. ABD83939), Elaeis guineensis fatty acyl-ACPthioesterase (GenBank Acc. No. AAD42220), Populus tomentosa fattyacyl-ACP thioesterase (GenBank Acc. No. ABC47311), Arabidopsis thalianafatty acyl-ACP thioesterase (GenBank Acc. No. NP_172327), Arabidopsisthaliana fatty acyl-ACP thioesterase (GenBank Acc. No. CAA85387),Arabidopsis thaliana fatty acyl-ACP thioesterase (GenBank Acc. No.CAA85388), Gossypium hirsutum fatty acyl-ACP thioesterase (GenBank Acc.No. Q9SQI3), Cuphea lanceolata fatty acyl-ACP thioesterase (GenBank Acc.No. CAA54060), Cuphea hookeriana fatty acyl-ACP thioesterase (GenBankAcc. No. AAC72882), Cuphea calophylla subsp. mesostemon fatty acyl-ACPthioesterase (GenBank Acc. No. ABB71581), Cuphea lanceolata fattyacyl-ACP thioesterase (GenBank Acc. No. CAC19933), Elaeis guineensisfatty acyl-ACP thioesterase (GenBank Acc. No. AAL15645), Cupheahookeriana fatty acyl- ACP thioesterase (GenBank Acc. No. Q39513),Gossypium hirsutum fatty acyl-ACP thioesterase (GenBank Acc. No.AAD01982), Vitis vinifera fatty acyl-ACP thioesterase (GenBank Acc. No.CAN81819), Garcinia mangostana fatty acyl-ACP thioesterase (GenBank Acc.No. AAB51525), Brassica juncea fatty acyl-ACP thioesterase (GenBank Acc.No. ABI18986), Madhuca longifolia fatty acyl-ACP thioesterase (GenBankAcc. No. AAX51637), Brassica napus fatty acyl-ACP thioesterase (GenBankAcc. No. ABH11710), Brassica napus fatty acyl-ACP thioesterase (GenBankAcc. No. CAA52070.1), Oryza sativa (indica cultivar-group) fattyacyl-ACP thioesterase (GenBank Acc. No. EAY86877), Oryza sativa(japonica cultivar-group) fatty acyl-ACP thioesterase (GenBank Acc. No.NP_001068400), Oryza sativa (indica cultivar-group) fatty acyl-ACPthioesterase (GenBank Acc. No. EAY99617), Cuphea hookeriana fattyacyl-ACP thioesterase (GenBank Acc. No. AAC49269), Ulmus Americana fattyacyl-ACP thioesterase (GenBank Acc. No. AAB71731), Cuphea lanceolatafatty acyl-ACP thioesterase (GenBank Acc. No. CAB60830), Cupheapalustris fatty acyl-ACP thioesterase (GenBank Acc. No. AAC49180), Irisgermanica fatty acyl-ACP thioesterase (GenBank Acc. No. AAG43858, Irisgermanica fatty acyl-ACP thioesterase (GenBank Acc. No. AAG43858.1),Cuphea palustris fatty acyl-ACP thioesterase (GenBank Acc. No.AAC49179), Myristica fragrans fatty acyl-ACP thioesterase (GenBank Acc.No. AAB71729), Myristica fragrans fatty acyl-ACP thioesterase (GenBankAcc. No. AAB717291.1), Cuphea hookeriana fatty acyl-ACP thioesteraseGenBank Acc. No. U39834), Umbelluaria californica fatty acyl-ACPthioesterase (GenBank Acc. No. M94159), Cinnamomum camphora fattyacyl-ACP thioesterase (GenBank Acc. No. U31813), Ricinus communis fattyacyl-ACP thioesterase (GenBank Acc. No. ABS30422.1), Helianthus annuusacyl-ACP thioesterase (GenBank Accession No. AAL79361.1), Jatrophacurcas acyl-ACP thioesterase (GenBank Accession No. ABX82799.3), Zeamays oleoyl-acyl carrier protein thioesterase, (GenBank Accession No.ACG40089.1), Haematococcus pluvialis fatty acyl- ACP thioesterase(GenBank Accession No. HM560034.1) Desaturase Enzymes Linumusitatissimum fatty acid desaturase 3C, (GenBank Acc. No. ADV92272.1),Ricinus communis omega-3 fatty acid desaturase, endoplasmic reticulum,putative, (GenBank Acc. No. EEF36775.1), Vernicia fordii omega-3 fattyacid desaturase, (GenBank Acc. No. AAF12821), Glycine max chloroplastomega 3 fatty acid desaturase isoform 2, (GenBank Acc. No. ACF19424.1),Prototheca moriformis FAD-D omega 3 desaturase (SEQ ID NO: 35),Prototheca moriformis linoleate desaturase (SEQ ID NO: 36), Carthamustinctorius delta 12 desaturase, (GenBank Accession No. ADM48790.1),Gossypium hirsutum omega-6 desaturase, (GenBank Accession No.CAA71199.1), Glycine max microsomal desaturase (GenBank Accession No.BAD89862.1), Zea mays fatty acid desaturase (GenBank Accession No.ABF50053.1), Brassica napa linoleic acid desaturase (GenBank AccessionNo. AAA32994.1), Camelina sativa omega-3 desaturase (SEQ ID NO: 37),Prototheca moriformis delta 12 desaturase allele 2 (SEQ ID NO: 38,Camelina sativa omega-3 FAD7-1 (SEQ ID NO: 39), Helianthus annuusstearoyl-ACP desaturase, (GenBank Accession No. AAB65145.1), Ricinuscommunis stearoyl-ACP desaturase, (GenBank Accession No. AACG59946.1),Brassica juncea plastidic delta-9-stearoyl-ACP desaturase (GenBankAccession No. AAD40245.1), Glycine max stearoyl-ACP desaturase (GenBankAccession No. ACJ39209.1), Olea europaea stearoyl-ACP desaturase(GenBank Accession No. AAB67840.1), Vernicia fordiistearoyl-acyl-carrier protein desaturase, (GenBank Accession No.ADC32803.1), Descurainia sophia delta-12 fatty acid desaturase (GenBankAccession No. ABS86964.2), Euphorbia lagascae delta12-oleic aciddesaturase (GenBank Acc. No. AAS57577.1), Chlorella vulgaris delta 12fatty acid desaturase (GenBank Accession No. ACF98528), Chlorellavulgaris omega-3 fatty acid desaturase (GenBank Accession No. BAB78717),Haematococcus pluvialis omega-3 fatty acid desaturase (GenBank AccessionNo. HM560035.1), Haematococcus pluvialis stearoyl-ACP-desaturase GenBankAccession No. EF586860.1, Haematococcus pluvialisstearoyl-ACP-desaturase GenBank Accession No. EF523479.1 Oleate12-hydroxylase Enzymes Ricinus communis oleate 12-hydroxylase (GenBankAcc. No. AAC49010.1), Physaria lindheimeri oleate 12-hydroxylase(GenBank Acc. No. ABQ01458.1), Physaria lindheimeri mutant bifunctionaloleate 12-hydroxylase: desaturase (GenBank Acc. No. ACF17571.1),Physaria lindheimeri bifunctional oleate 12-hydroxylase: desaturase(GenBank Accession No. ACQ42234.1), Physaria lindheimeri bifunctionaloleate 12- hydroxylase: desaturase (GenBank Acc. No. AAC32755.1),Arabidopsis lyrata subsp. Lyrata (GenBank Acc. No. XP_002884883.1)Glycerol-3-phosphate Enzymes Arabidopsis thaliana glycerol-3-phosphateacyltransferase BAA00575, Chlamydomonas reinhardtii glycerol-3-phosphateacyltransferase (GenBank Acc. No. EDP02129), Chlamydomonas reinhardtiiglycerol-3-phosphate acyltransferase (GenBank Acc. No. Q886Q7),Cucurbita moschata acyl-(acyl-carrier-protein): glycerol-3-phosphateacyltransferase (GenBank Acc. No. BAB39688), Elaeis guineensisglycerol-3-phosphate acyltransferase, ((GenBank Acc. No. AAF64066),Garcina mangostana glycerol-3-phosphate acyltransferase (GenBank Acc.No. ABS86942), Gossypium hirsutum glycerol-3-phosphate acyltransferase(GenBank Acc. No. ADK23938), Jatropha curcas glycerol-3-phosphateacyltransferase (GenBank Acc. No. ADV77219), Jatropha curcas plastidglycerol-3- phosphate acyltransferase (GenBank Acc. No. ACR61638),Ricinus communis plastidial glycerol-phosphate acyltransferase (GenBankAcc. No. EEF43526), Vica faba glycerol-3- phosphate acyltransferase(GenBank Accession No. AAD05164), Zea mays glycerol-3- phosphateacyltransferase (GenBank Acc. No. ACG45812) Lysophosphatidic acidacyltransferase Enzymes Arabidopsis thaliana1-acyl-sn-glycerol-3-phosphate acyltransferase (GenBank Accession No.AEE85783), Brassica juncea 1-acyl-sn-glycerol-3-phosphateacyltransferase (GenBank Accession No. ABQ42862), Brassica juncea1-acyl-sn-glycerol-3-phosphate acyltransferase (GenBank Accession No.ABM92334), Brassica napus 1-acyl-sn-glycerol-3-phosphate acyltransferase(GenBank Accession No. CAB09138), Chlamydomonas reinhardtiilysophosphatidic acid acyltransferase (GenBank Accession No. EDP02300),Cocos nucifera lysophosphatidic acid acyltransferase (GenBank Acc. No.AAC49119), Limnanthes alba lysophosphatidic acid acyltransferase(GenBank Accession No. EDP02300), Limnanthes douglasii1-acyl-sn-glycerol-3-phosphate acyltransferase (putative) (GenBankAccession No. CAA88620), Limnanthes douglasii acyl-CoA:sn-1-acylglycerol-3-phosphate acyltransferase (GenBank Accession No.ABD62751), Limnanthes douglasii 1-acylglycerol-3-phosphate O-acyltransferase (GenBank Accession No. CAA58239), Ricinus communis1-acyl-sn-glycerol- 3-phosphate acyltransferase (GenBank Accession No.EEF39377) Diacylglycerol acyltransferase Enzymes Arabidopsis thalianadiacylglycerol acyltransferase (GenBank Acc. No. CAB45373), Brassicajuncea diacylglycerol acyltransferase (GenBank Acc. No. AAY40784),Elaeis guineensis putative diacylglycerol acyltransferase (GenBank Acc.No. AEQ94187), Elaeis guineensis putative diacylglycerol acyltransferase(GenBank Acc. No. AEQ94186), Glycine max acyl CoA: diacylglycerolacyltransferase (GenBank Acc. No. AAT73629), Helianthus annusdiacylglycerol acyltransferase (GenBank Acc. No. ABX61081), Oleaeuropaea acyl- CoA: diacylglycerol acyltransferase 1 (GenBank Acc. No.AAS01606), Ricinus communis diacylglycerol acyltransferase (GenBank Acc.No. AAR11479) Phospholipid diacylglycerol acyltransferase EnzymesArabidopsis thaliana phospholipid: diacylglycerol acyltransferase(GenBank Acc. No. AED91921), Elaeis guineensis putative phospholipid:diacylglycerol acyltransferase (GenBank Acc. No. AEQ94116), Glycine maxphospholipid: diacylglycerol acyltransferase 1-like (GenBank Acc. No.XP_003541296), Jatropha curcas phospholipid: diacylglycerolacyltransferase (GenBank Acc. No. AEZ56255), Ricinus communisphospholipid: diacylglycerol acyltransferase (GenBank Acc. No.ADK92410), Ricinus communis phospholipid: diacylglycerol acyltransferase(GenBank Acc. No. AEW99982)

Example 10 Engineering Chlorella Sorokiniana

Expression of recombinant genes in accordance with the present inventionin Chlorella sorokiniana can be accomplished by modifying the methodsand vectors taught by Dawson et al. as discussed herein. Briefly, Dawsonet al., Current Microbiology Vol. 35 (1997) pp. 356-362, reported thestable nuclear transformation of Chlorella sorokiniana with plasmid DNA.Using the transformation method of microprojectile bombardment, Dawsonintroduced the plasmid pSV72-NRg, encoding the full Chlorella vulgarisnitrate reductase gene (NR, GenBank Accession No. U39931), into mutantChlorella sorokiniana (NR-mutants). The NR-mutants are incapable ofgrowth without the use of nitrate as a source of nitrogen. Nitratereductase catalyzes the conversion of nitrate to nitrite. Prior totransformation, Chlorella sorokiniana NR-mutants were unable to growbeyond the microcolony stage on culture medium comprising nitrate (NO₃⁻) as the sole nitrogen source. The expression of the Chlorella vulgarisNR gene product in NR-mutant Chlorella sorokiniana was used as aselectable marker to rescue the nitrate metabolism deficiency. Upontransformation with the pSV72-NRg plasmid, NR-mutant Chlorellasorokiniana stably expressing the Chlorella vulgaris NR gene productwere obtained that were able to grow beyond the microcolony stage onagar plates comprising nitrate as the sole carbon source. Evaluation ofthe DNA of the stable transformants was performed by Southern analysisand evaluation of the RNA of the stable transformants was performed byRNase protection. Selection and maintenance of the transformed Chlorellasorokiniana (NR mutant) was performed on agar plates (pH 7.4) comprising0.2 g/L MgSO₄, 0.67 g/L KH₂PO₄, 3.5 g/L K₂HPO₄, 1.0 g/L Na₃C₆H₅O₇.H₂Oand 16.0 g/L agar, an appropriate nitrogen source (e.g., NO₃),micronutrients, and a carbon source. Dawson also reported thepropagation of Chlorella sorokiniana and Chlorella sorokiniana NRmutants in liquid culture medium. Dawson reported that the plasmidpSV72-NRg and the promoter and 3′ UTR/terminator of the Chlorellavulgaris nitrate reductase gene were suitable to enable heterologousgene expression in Chlorella sorokiniana NR-mutants. Dawson alsoreported that expression of the Chlorella vulgaris nitrate reductasegene product was suitable for use as a selectable marker in Chlorellasorokiniana NR-mutants.

In an embodiment of the present invention, vector pSV72-NRg, comprisingnucleotide sequence encoding the Chlorella vulgaris nitrate reductase(CvNR) gene product for use as a selectable marker, is constructed andmodified to further comprise a lipid biosynthesis pathway expressioncassette sequence, thereby creating a transformation vector. The lipidbiosynthesis pathway expression cassette encodes one or more lipidbiosynthesis pathway proteins selected from Table 20, eachprotein-coding sequence codon-optimized for expression in Chlorellasorokiniana to reflect the codon bias inherent in nuclear genes ofChlorella sorokiniana in accordance with Tables 19A-D. For each lipidbiosynthesis pathway protein of Table 20, the codon-optimized genesequence can individually be operably linked to the CvNR promoterupstream of the protein-coding sequence and operably linked to the CvNR3′UTR/terminator at the 3′ region, or downstream, of the protein-codingsequence. The transformation construct may additionally comprisehomology regions to the Chlorella sorokiniana genome for targetedgenomic integration of the transformation vector. Homology regions maybe selected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. Stable transformation of Chlorellasorokiniana with the transformation vector is achieved throughwell-known transformation techniques including microprojectilebombardment or other known methods. Activity of the CvNR gene productcan be used as a selectable marker to rescue the nitrogen assimilationdeficiency of Chlorella sorokiniana NR mutant strains and to select forChlorella sorokiniana NR-mutants stably expressing the transformationvector. Growth media suitable for Chlorella sorokiniana lipid productioninclude, but are not limited to 0.5 g/L KH₂PO₄, 0.5 g/L K₂HPO₄, 0.25 g/LMgSO₄-7H2O, with supplemental micronutrients and the appropriatenitrogen and carbon sources (Patterson, Lipids Vol. 5:7 (1970), pp.597-600). Evaluation of fatty acid profiles of Chlorella sorokinianalipids can be assessed through standard lipid extraction and analyticalmethods described herein.

Example 11 Engineering Chlorella Vulgaris

Expression of recombinant genes in accordance with the present inventionin Chlorella vulgaris can be accomplished by modifying the methods andvectors taught by Chow and Tung et al. as discussed herein. Briefly,Chow and Tung et al., Plant Cell Reports, Volume 18 (1999), pp. 778-780,reported the stable nuclear transformation of Chlorella vulgaris withplasmid DNA. Using the transformation method of electroporation, Chowand Tung introduced the plasmid pIG121-Hm (GenBank Accession No.AB489142) into Chlorella vulgaris. The nucleotide sequence of pIG121-Hmcomprised sequence encoding a beta-glucuronidase (GUS) reporter geneproduct operably-linked to a CaMV 35S promoter upstream of the GUSprotein-coding sequence and further operably linked to the 3′UTR/terminator of the nopaline synthase (nos) gene downstream of the GUSprotein-coding sequence. The sequence of plasmid pIG121-Hm furthercomprised a hygromycin B antibiotic resistance cassette. This hygromycinB antibiotic resistance cassette comprised a CaMV 35S promoter operablylinked to sequence encoding the hygromycin phosphotransferase (hpt,GenBank Accession No. BAH24259) gene product. Prior to transformation,Chlorella vulgaris was unable to be propagated in culture mediumcomprising 50 ug/ml hygromycin B. Upon transformation with the pIG121-Hmplasmid, transformants of Chlorella vulgaris were obtained that werepropagated in culture medium comprising 50 ug/ml hygromycin B. Theexpression of the hpt gene product in Chlorella vulgaris enabledpropagation of transformed Chlorella vulgaris in the presence of 50ug/mL hygromycin B, thereby establishing the utility of the a hygromycinB resistance cassette as a selectable marker for use in Chlorellavulgaris. Detectable activity of the GUS reporter gene indicated thatCaMV 35S promoter and nos 3′UTR are suitable for enabling heterologousgene expression in Chlorella vulgaris. Evaluation of the genomic DNA ofthe stable transformants was performed by Southern analysis. Selectionand maintenance of transformed Chlorella vulgaris was performed on agarplates comprising YA medium (agar and 4 g/L yeast extract). Thepropagation of Chlorella vulgaris in liquid culture medium was conductedas discussed by Chow and Tung. Propagation of Chlorella vulgaris inmedia other than YA medium has been described (for examples, see Chaderet al., Revue des Energies Renouvelabes, Volume 14 (2011), pp. 21-26 andIllman et al., Enzyme and Microbial Technology, Vol. 27 (2000), pp.631-635). Chow and Tung reported that the plasmid pIG121-Hm, the CaMV35S promoter, and the Agrobacterium tumefaciens nopaline synthase gene3′UTR/terminator are suitable to enable heterologous gene expression inChlorella vulgaris. In addition, Chow and Tung reported the hygromycin Bresistance cassette was suitable for use as a selectable marker inChlorella vulgaris. Additional plasmids, promoters, 3′UTR/terminators,and selectable markers suitable for enabling heterologous geneexpression in Chlorella vulgaris have been discussed in Chader et al.,Revue des Energies Renouvelabes, Volume 14 (2011), pp. 21-26.

In an embodiment of the present invention, pIG121-Hm, comprising thenucleotide sequence encoding the hygromycin B gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Chlorella vulgaris to reflect thecodon bias inherent in nuclear genes of Chlorella vulgaris in accordancewith Tables 19A-D. For each lipid biosynthesis pathway protein of Table20, the codon-optimized gene sequence can individually be operablylinked to the CaMV 35S promoter upstream of the protein-coding sequenceand operably linked to the Agrobacterium tumefaciens nopaline synthasegene 3′UTR/terminator at the 3′ region, or downstream, of theprotein-coding sequence. The transformation construct may additionallycomprise homology regions to the Chlorella vulgaris genome for targetedgenomic integration of the transformation vector. Homology regions maybe selected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. Stable transformation of Chlorella vulgariswith the transformation vector is achieved through well-knowntransformation techniques including electroporation or other knownmethods. Activity of the hygromycin B resistance gene product can beused as a marker to select for Chlorella vulgaris transformed with thetransformation vector on, but not limited to, agar medium comprisinghygromycin. Growth media suitable for Chlorella vulgaris lipidproduction include, but are not limited to BG11 medium (0.04 g/L KH₂PO₄,0.075 g/L CaCl₂, 0.036 g/L citric acid, 0.006 g/L Ammonium FerricCitrate, 1 mg/L EDTA, and 0.02 g/L Na₂CO₃) supplemented with tracemetals, and optionally 1.5 g/L NaNO3. Additional media suitable forculturing Chlorella vulgaris for lipid production include, for example,Watanabe medium (comprising 1.5 g/L KNO₃, 1.25 g/L KH₂PO₄, 1.25 g l⁻¹MgSO₄.7H₂O, 20 mg l⁻¹ FeSO₄.7H₂O with micronutrients and low-nitrogenmedium (comprising 203 mg/l (NH₄)₂HPO₄, 2.236 g/l KCl, 2.465 g/l MgSO₄,1.361 g/l KH₂PO₄ and 10 mg/l FeSO₄) as reported by Illman et al., Enzymeand Microbial Technology, Vol. 27 (2000), pp. 631-635. Evaluation offatty acid profiles of Chlorella vulgaris lipids can be assessed throughstandard lipid extraction and analytical methods described herein.

Example 12 Engineering Chlorella Ellipsoidea

Expression of recombinant genes in accordance with the present inventionin Chlorella ellipsoidea can be accomplished by modifying the methodsand vectors taught by Chen et al. as discussed herein. Briefly, Chen etal., Current Genetics, Vol. 39:5 (2001), pp. 365-370, reported thestable transformation of Chlorella ellipsoidea with plasmid DNA. Usingthe transformation method of electroporation, Chen introduced theplasmid pBinUΩNP-1 into Chlorella ellipsoidea. The nucleotide sequenceof pBinUΩNP-1 comprised sequence encoding the neutrophil peptide-1(NP-1) rabbit gene product operably linked to a Zea mays Ubiquitin(ubi1) gene promoter upstream of the NP-1 protein-coding region andoperably linked to the 3′ UTR/terminator of the nopaline synthase (nos)gene downstream of the NP-1 protein-coding region. The sequence ofplasmid pBinUΩNP-1 further comprised a G418 antibiotic resistancecassette. This G418 antibiotic resistance cassette comprised sequenceencoding the aminoglycoside 3′-phosphotransferase (aph 3′) gene product.The aph 3′ gene product confers resistance to the antibiotic G418. Priorto transformation, Chlorella ellipsoidea was unable to be propagated inculture medium comprising 30 ug/mL G418. Upon transformation with thepBinUΩNP-1 plasmid, transformants of Chlorella ellipsoidea were obtainedthat were propagated in selective culture medium comprising 30 ug/mLG418. The expression of the aph 3′ gene product in Chlorella ellipsoideaenabled propagation of transformed Chlorella ellipsoidea in the presenceof 30 ug/mL G418, thereby establishing the utility of the G418antibiotic resistance cassette as selectable marker for use in Chlorellaellipsoidea. Detectable activity of the NP-1 gene product indicated thatthe ubi 1 promoter and nos 3′ UTR are suitable for enabling heterologousgene expression in Chlorella ellipsoidea. Evaluation of the genomic DNAof the stable transformants was performed by Southern analysis.Selection and maintenance of the transformed Chlorella ellipsoidea wasperformed on Knop medium (comprising 0.2 g/L K₂HPO₄, 0.2 g/L MgSO₄.7H₂O,0.12 g/L KCl, and 10 mg/L FeCl3, pH 6.0-8.0 supplemented with 0.1% yeastextract and 0.2% glucose) with 15 ug/mL G418 (for liquid cultures) orwith 30 ug/mL G418 (for solid cultures comprising 1.8% agar).Propagation of Chlorella ellipsoidea in media other than Knop medium hasbeen reported (see Cho et al., Fisheries Science, Vol. 73:5 (2007), pp.1050-1056, Jarvis and Brown, Current Genetics, Vol. 19 (1991), pp.317-321 and Kim et al., Marine Biotechnology, Vol. 4 (2002), pp.63-'73). Additional plasmids, promoters, 3′UTR/terminators, andselectable markers suitable for enabling heterologous gene expression inChlorella ellipsoidea have been reported (see Jarvis and Brown and Kimet al., Marine Biotechnology, Vol. 4 (2002), pp. 63-73). Chen reportedthat the plasmid pBinUΩNP-1, the ubil promoter, and the Agrobacteriumtumefaciens nopaline synthase gene 3′UTR/terminator are suitable toenable exogenous gene expression in Chlorella ellipsoidea. In addition,Chen reported that the G418 resistance cassette encoded on pBinUΩNP-1was suitable for use as a selectable marker in Chlorella ellipsoidea.

In an embodiment of the present invention, vector pBinUΩNP-1, comprisingthe nucleotide sequence encoding the aph 3′ gene product, conferringresistance to G418, for use as a selectable marker, is constructed andmodified to further comprise a lipid biosynthesis pathway expressioncassette sequence, thereby creating a transformation vector. The lipidbiosynthesis pathway expression cassette encodes one or more lipidbiosynthesis pathway proteins selected from Table 20, eachprotein-coding sequence codon-optimized for expression in Chlorellaellipsoidea to reflect the codon bias inherent in nuclear genes ofChlorella ellipsoidea in accordance with Tables 19A-D. For each lipidbiosynthesis pathway protein of Table 20, the codon-optimized genesequence can individually be operably linked to the Zea mays ubilpromoter upstream of the protein-coding sequence and operably linked tothe Agrobacterium tumefaciens nopaline synthase gene 3′UTR/terminator atthe 3′ region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Chlorella ellipsoidea genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Chlorella ellipsoidea with the transformationvector is achieved through well-known transformation techniquesincluding electroporation or other known methods. Activity of the aph 3′gene product can be used as a marker to select for Chlorella ellipsoideatransformed with the transformation vector on, but not limited to, Knopagar medium comprising G418. Growth media suitable for Chlorellaellipsoidea lipid production include, but are not limited to, Knopmedium and those culture medium reported by Jarvis and Brown and Kim etal. Evaluation of fatty acid profiles of Chlorella ellipsoidea lipidscan be assessed through standard lipid extraction and analytical methodsdescribed herein.

Example 13 Engineering Chlorella Kessleri

Expression of recombinant genes in accordance with the present inventionin Chlorella kessleri can be accomplished by modifying the methods andvectors taught by El-Sheekh et al. as discussed herein. Briefly,El-Sheekh et al., Biologia Plantarium, Vol. 42:2 (1999), pp. 209-216,reported the stable transformation of Chlorella kessleri with plasmidDNA. Using the transformation method of microprojectile bombardment,El-Sheekh introduced the plasmid pBI121 (GenBank Accession No. AF485783)into Chlorella kessleri. Plasmid pBI121 comprised a kanamycin/neomycinantibiotic resistance cassette. This kanamycin/neomycin antibioticresistance cassette comprised the Agrobacterium tumefaciens nopalinesynthase (nos) gene promoter, sequence encoding the neomycinphosphotransferase II (nptII) gene product (GenBank Accession No.AAL92039) for resistance to kanamycin and G418, and the 3′UTR/terminator of the Agrobacterium tumefaciens nopaline synthase (nos)gene. pBI121 further comprised sequence encoding a beta-glucuronidase(GUS) reporter gene product operably linked to a CaMV 35S promoter andoperably linked to a 3′ UTR/terminator of the nos gene. Prior totransformation, Chlorella kessleri was unable to be propagated inculture medium comprising 15 ug/L kanamycin. Upon transformation withthe pBI121plasmid, transformants of Chlorella kessleri were obtainedthat were propagated in selective culture medium comprising 15 mg/Lkanamycin. The express ion of the nptII gene product in Chlorellakessleri enabled propagation in the presence of 15 mg/L kanamycin,thereby establishing the utility of the kanamycin/neomycin antibioticresistance cassette as selectable marker for use in Chlorella kessleri.Detectable activity of the GUS gene product indicated that the CaMV 35Spromoter and nos 3′ UTR are suitable for enabling heterologous geneexpression in Chlorella kessleri. Evaluation of the genomic DNA of thestable transformants was performed by Southern analysis. As reported byEl-Sheekh, selection and maintenance of transformed Chlorella kessleriwas conducted on semisolid agar plates comprising YEG medium (1% yeastextract, 1% glucose) and 15 mg/L kanamycin. El-Sheekh also reported thepropagation of Chlorella kessleri in YEG liquid culture media.Additional media suitable for culturing Chlorella kessleri for lipidproduction are disclosed in Sato et al., BBA Molecular and Cell Biologyof Lipids, Vol. 1633 (2003), pp. 27-34). El-Sheekh reported that theplasmid pBI121, the CaMV promoter, and the nopaline synthase gene3′UTR/terminator are suitable to enable heterologous gene expression inChlorella kessleri. In addition, El-Sheekh reported that thekanamycin/neomycin resistance cassette encoded on pBI121 was suitablefor use as a selectable marker in Chlorella kessleri.

In an embodiment of the present invention, vector pBI121, comprising thenucleotide sequence encoding the kanamycin/neomycin resistance geneproduct for use as a selectable marker, is constructed and modified tofurther comprise a lipid biosynthesis pathway expression cassettesequence, thereby creating a transformation vector. The lipidbiosynthesis pathway expression cassette encodes one or more lipidbiosynthesis pathway proteins selected from Table 20, eachprotein-coding sequence codon-optimized for expression in Chlorellakessleri to reflect the codon bias inherent in nuclear genes ofChlorella kessleri in accordance with Tables 19A-D. For each lipidbiosynthesis pathway protein of Table 20, the codon-optimized genesequence can individually be operably linked to the CaMV 35S promoterupstream of the protein-coding sequence and operably linked to theAgrobacterium tumefaciens nopaline synthase gene 3′UTR/terminator at the3′ region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Chlorella kessleri genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Chlorella kessleri with the transformationvector is achieved through well-known transformation techniquesincluding microprojectile bombardment or other known methods. Activityof the nptII gene product can be used as a marker to select forChlorella kessleri transformed with the transformation vector on, butnot limited to, YEG agar medium comprising kanamycin or neomycin. Growthmedia suitable for Chlorella kessleri lipid production include, but arenot limited to, YEG medium, and those culture media reported by Sato etal. Evaluation of fatty acid profiles of Chlorella kessleri lipids canbe assessed through standard lipid extraction and analytical methodsdescribed herein.

Example 14 Engineering Dunaliella Tertiolecta

Expression of recombinant genes in accordance with the present inventionin Dunaliella tertiolecta can be accomplished by modifying the methodsand vectors taught by Walker et al. as discussed herein. Briefly, Walkeret al., Journal of Applied Phycology, Vol. 17 (2005), pp. 363-368,reported stable nuclear transformation of Dunaliella tertiolecta withplasmid DNA. Using the transformation method of electroporation, Walkerintroduced the plasmid pDbleFLAG1.2 into Dunaliella tertiolecta.pDbleFLAG1.2 comprised sequence encoding a bleomycin antibioticresistance cassette, comprising sequence encoding the Streptoalloteichushindustanus Bleomycin binding protein (ble), for resistance to theantibiotic phleomycin, operably linked to the promoter and 3′ UTR of theDunaliella tertiolecta ribulose-1,5-bisphosphate carboxylase/oxygenasesmall subunit gene (rbcS1, GenBank Accession No. AY530155). Prior totransformation, Dunaliella tertiolecta was unable to be propagated inculture medium comprising 1 mg/L phleomycin. Upon transformation withthe pDbleFLAG1.2 plasmid, transformants of Dunaliella tertiolecta wereobtained that were propagated in selective culture medium comprising 1mg/L phleomycin. The expression of the ble gene product in Dunaliellatertiolecta enabled propagation in the presence of 1 mg/L phleomycin,thereby establishing the utility of the bleomycin antibiotic resistancecassette as selectable marker for use in Dunaliella tertiolecta.Evaluation of the genomic DNA of the stable transformants was performedby Southern analysis. As reported by Walker, selection and maintenanceof transformed Dunaliella tertiolecta was conducted in Dunaliella medium(DM, as described by Provasoli et al., Archiv fur Mikrobiologie, Vol. 25(1957), pp. 392-428) further comprising 4.5 g/L NaCl and 1 mg/Lpheomycin. Additional media suitable for culturing Dunaliellatertiolecta for lipid production are discussed in Takagi et al., Journalof Bioscience and Bioengineering, Vol. 101:3 (2006), pp. 223-226 and inMassart and Hanston, Proceedings Venice 2010, Third InternationalSymposium on Energy from Biomass and Waste. Walker reported that theplasmid pDbleFLAG1.2 and the promoter and 3′ UTR of the Dunaliellatertiolecta ribulose-1,5-bisphosphate carboxylase/oxygenase smallsubunit gene are suitable to enable heterologous expression inDunaliella tertiolecta. In addition, Walker reported that the bleomycinresistance cassette encoded on pDbleFLAG1.2 was suitable for use as aselectable marker in Dunaliella tertiolecta.

In an embodiment of the present invention, vector pDbleFLAG1.2,comprising the nucleotide sequence encoding the ble gene product for useas a selectable marker, is constructed and modified to further comprisea lipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Dunaliella tertiolecta to reflect thecodon bias inherent in nuclear genes of Dunaliella tertiolecta inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the rbcS1 promoter upstream of the protein-codingsequence and operably linked to the rbcS1 3′UTR/terminator at the 3′region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Dunaliella tertiolecta genome for targeted genomic integration ofthe transformation vector. Homology regions may be selected to disruptone or more genomic sites of endogenous lipid biosynthesis pathwaygenes. Stable transformation of Dunaliella tertiolecta with thetransformation vector is achieved through well-known transformationtechniques including electroporation or other known methods. Activity ofthe ble gene product can be used as a marker to select for Dunaliellatertiolecta transformed with the transformation vector on, but notlimited to, DM medium comprising pheomycin. Growth medium suitable forDunaliella tertiolecta lipid production include, but are not limited toDM medium and those culture media described by Takagi et al. and Massartand Hanston. Evaluation of fatty acid profiles of Dunaliella tertiolectalipids can be assessed through standard lipid extraction and analyticalmethods described herein.

Example 15 Engineering Volvox Carteri

Expression of recombinant genes in accordance with the present inventionin Volvox carteri can be accomplished by modifying the methods andvectors taught by Hallman and Rappel et al. as discussed herein.Briefly, Hallman and Rappel et al., The Plant Journal, Volume 17 (1999),pp. 99-109, reported the stable nuclear transformation of Volvox carteriwith plasmid DNA. Using the transformation method of microprojectilebombardment, Hallman and Rappel introduced the pzeoE plasmid into Volvoxcarteri. The pzeoE plasmid comprised sequence encoding a bleomycinantibiotic resistance cassette, comprising sequence encoding theStreptoalloteichus hindustanus Bleomycin binding protein (ble), forresistance to the antibiotic zeocin, operably linked to and the promoterand 3′ UTR of the Volvox carteri beta-tubulin gene (GenBank AccessionNo. L24547). Prior to transformation, Volvox carteri was unable to bepropagated in culture medium comprising 1.5 ug/ml zeocin. Upontransformation with the pzeoE plasmid, transformants of Volvox carteriwere obtained that were propagated in selective culture mediumcomprising greater than 20 ug/ml zeocin. The expression of the ble geneproduct in Volvox carteri enabled propagation in the presence of 20ug/ml zeocin, thereby establishing the utility of the bleomycinantibiotic resistance cassette as selectable marker for use in Volvoxcarteri. Evaluation of the genomic DNA of the stable transformants wasperformed by Southern analysis. As reported by Hallman and Rappel,selection and maintenance of transformed Volvox carteri was conducted inVolvox medium (VM, as described by Provasoli and Pintner, The Ecology ofAlgae, Special Publication No. 2 (1959), Tyron, C. A. and Hartman, R.T., eds., Pittsburgh: University of Pittsburgh, pp. 88-96) with 1 mg/Lpheomycin. Media suitable for culturing Volvox carteri for lipidproduction are also discussed by Starr in Starr R, C., Dev Biol Suppl.,Vol. 4 (1970), pp. 59-100). Hallman and Rappel reported that the plasmidpzeoE and the promoter and 3′ UTR of the Volvox carteri beta-tubulingene are suitable to enable heterologous expression in Volvox carteri.In addition, Hallman and Rappel reported that the bleomycin resistancecassette encoded on pzeoE was suitable for use as a selectable marker inVolvox carteri. Additional plasmids, promoters, 3′UTR/terminators, andselectable markers suitable for enabling heterologous gene expression inVolvox carteri and suitable for use as selective markers Volvox carteriin have been reported (for instance see Hallamann and Sumper,Proceedings of the National Academy of Sciences, Vol. 91 (1994), pp11562-11566 and Hallman and Wodniok, Plant Cell Reports, Volume 25(2006), pp. 582-581).

In an embodiment of the present invention, vector pzeoE, comprising thenucleotide sequence encoding the ble gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 19, each protein-coding sequencecodon-optimized for expression in Volvox carteri to reflect the codonbias inherent in nuclear genes of Volvox carteri in accordance withTables 19A-D. For each lipid biosynthesis pathway protein of Table 20,the codon-optimized gene sequence can individually be operably linked tothe Volvox carteri beta-tubulin promoter upstream of the protein-codingsequence and operably linked to the Volvox carteri beta-tubulin3′UTR/terminator at the 3′ region, or downstream, of the protein-codingsequence. The transformation construct may additionally comprisehomology regions to the Volvox carteri genome for targeted genomicintegration of the transformation vector. Homology regions may beselected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. One skilled in the art can identify suchhomology regions within the sequence of the Volvox carteri genome(referenced in the publication by Prochnik et al., Science, Vol.329:5988 (2010), pp223-226). Stable transformation of Volvox carteriwith the transformation vector is achieved through well-knowntransformation techniques including microprojectile bombardment or otherknown methods. Activity of the ble gene product can be used as a markerto select for Volvox carteri transformed with the transformation vectoron, but not limited to, VM medium comprising zeocin. Growth mediumsuitable for Volvox carteri lipid production include, but are notlimited to VM medium and those culture media discussed by Starr.Evaluation of fatty acid profiles of Volvox carteri lipids can beassessed through standard lipid extraction and analytical methodsdescribed herein.

Example 16 Engineering Haematococcus Pluvialis

Expression of recombinant genes in accordance with the present inventionin Haematococcus pluvialis can be accomplished by modifying the methodsand vectors taught by Steinbrenner and Sandmann et al. as discussedherein. Briefly, Steinbrenner and Sandmann et al., Applied andEnvironmental Microbiology, Vol. 72:12 (2006), pp. 7477-7484, reportedthe stable nuclear transformation of Haematococcus pluvialis withplasmid DNA. Using the transformation method of microprojectilebombardment, Steinbrenner introduced the plasmid pPlat-pds-L504R intoHaematococcus pluvialis. The plasmid pPlat-pds-L504R comprised anorflurazon resistance cassette, which comprised the promoter,protein-coding sequence, and 3′UTR of the Haematococcus pluvialisphytoene desaturase gene (Pds, GenBank Accession No. AY781170), whereinthe protein-coding sequence of Pds was modified at position 504 (therebychanging a leucine to an arginine) to encode a gene product (Pds-L504R)that confers resistance to the herbicide norflurazon. Prior totransformation with pPlat-pds-L504R, Haematococcus pluvialis was unableto propagate on medium comprising 5 uM norflurazon. Upon transformationwith the pPlat-pds-L504R plasmid, transformants of Haematococcuspluvialis were obtained that were propagated in selective culture mediumcomprising 5 uM norflurazon. The expression of the Pds-L504R geneproduct in Haematococcus pluvialis enabled propagation in the presenceof 5 uM norflurazon, thereby establishing the utility of the norflurazonherbicide resistance cassette as selectable marker for use inHaematococcus pluvialis. Evaluation of the genomic DNA of the stabletransformants was performed by Southern analysis. As reported bySteinbrenner, selection and maintenance of transformed Haematococcuspluvialis was conducted on agar plates comprising OHA medium (OHM (0.41g/L KNO₃, 0.03 g/L Na₂HPO₄, 0.246 g/L MgSO₄.7H₂O, 0.11 g/L CaCl₂.2H₂O,2.62 mg/L Fe_((III))citrate×H₂O, 0.011 mg/L CoCl₂.6H₂O, 0.012 mg/LCuSO₄.5H₂O, 0.075 mg/L Cr₂O₃, 0.98 mg/L MnCl₂.4H₂O, 0.12 mg/LNa₂MoO_(4×2)H₂O, 0.005 mg/L SeO₂ and 25 mg/L biotin, 17.5 mg/L thiamine,and 15 mg/L vitamin B12), supplemented with 2.42 g/L Tris-acetate, and 5mM norflurazon. Propagation of Haematococcus pluvialis in liquid culturewas performed by Steinbrenner and Sandmann using basal medium (basalmedium as described by Kobayashi et al., Applied and EnvironmentalMicrobiology, Vol. 59 (1993), pp. 867-873). Steinbrenner and Sandmannreported that the pPlat-pds-L504R plasmid and promoter and 3′ UTR of theHaematococcus pluvialis phytoene desaturase gene are suitable to enableheterologous expression in Haematococcus pluvialis. In addition,Steinbrenner and Sandmann reported that the norflurazon resistancecassette encoded on pPlat-pds-L504R was suitable for use as a selectablemarker in Haematococcus pluvialis. Additional plasmids, promoters,3′UTR/terminators, and selectable markers suitable for enablingheterologous gene expression in Haematococcus pluvialis have beenreported (see Kathiresan et al., Journal of Phycology, Vol. 45 (2009),pp 642-649).

In an embodiment of the present invention, vector pPlat-pds-L504R,comprising the nucleotide sequence encoding the Pds-L504R gene productfor use as a selectable marker, is constructed and modified to furthercomprise a lipid biosynthesis pathway expression cassette sequence,thereby creating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Haematococcus pluvialis to reflect thecodon bias inherent in nuclear genes of Haematococcus pluvialis inaccordance with Tables 19 A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Haematococcus pluvialis pds gene promoterupstream of the protein-coding sequence and operably linked to theHaematococcus pluvialis pds gene 3′UTR/terminator at the 3′ region, ordownstream, of the protein-coding sequence. The transformation constructmay additionally comprise homology regions to the Haematococcuspluvialis genome for targeted genomic integration of the transformationvector. Homology regions may be selected to disrupt one or more genomicsites of endogenous lipid biosynthesis pathway genes. Stabletransformation of Haematococcus pluvialis with the transformation vectoris achieved through well-known transformation techniques includingmicroprojectile bombardment or other known methods. Activity of thePds-L504R gene product can be used as a marker to select forHaematococcus pluvialis transformed with the transformation vector on,but not limited to, OHA medium comprising norflurazon. Growth mediasuitable for Haematococcus pluvialis lipid production include, but arenot limited to basal medium and those culture media described byKobayashi et al., Kathiresan et al, and Gong and Chen, Journal ofApplied Phycology, Vol. 9:5 (1997), pp. 437-444). Evaluation of fattyacid profiles of Haematococcus pluvialis lipids can be assessed throughstandard lipid extraction and analytical methods described herein.

Example 17 Engineering Closterium Peracerosum-Strigosum-LittoraleComplex

Expression of recombinant genes in accordance with the present inventionin Closterium peracerosum-strigosum-littorals complex can beaccomplished by modifying the methods and vectors taught by Abe et al.as discussed herein. Briefly, Abe et al., Plant Cell Physiology, Vol.52:9 (2011), pp. 1676-1685, reported the stable nuclear transformationof Closterium peracerosum-strigosum-littorals complex with plasmid DNA.Using the transformation methods of microprojectile bombardment, Abeintroduced the plasmid pSA106 into Closteriumperacerosum-strigosum-littorals complex. Plasmid pSA106 comprised ableomycin resistance cassette, comprising sequence encoding theStreptoalloteichus hindustanus Bleomycin binding protein gene (ble,GenBank Accession No. CAA37050) operably linked to the promoter and 3′UTR of the Closterium peracerosum-strigosum-littorals complexChlorophyll a/b-binding protein gene (CAB, GenBank Accession No.AB363403). Prior to transformation with pSA106, Closteriumperacerosum-strigosum-littorals complex was unable to propagate onmedium comprising 3 ug/ml phleomycin. Upon transformation with pSA106,transformants of Closterium peracerosum-strigosum-littorals complex wereobtained that were propagated in selective culture medium comprising 3ug/ml phleomycin. The expression of the ble gene product in Closteriumperacerosum-strigosum-littorals complex enabled propagation in thepresence of 3 ug/ml phleomycin, thereby establishing the utility of thebleomycin antibiotic resistance cassette as selectable marker for use inClosterium peracerosum-strigosum-littorals complex. Evaluation of thegenomic DNA of the stable transformants was performed by Southernanalysis. As reported by Abe, selection and maintenance of transformedClosterium peracerosum-strigosum-littorals complex was conducted firstin top agar with C medium (0.1 g/L KNO₃, 0.015 g/L Ca(NO₃)₂.4H2O, 0.05g/L glycerophosphate-Na2, 0.04 g/L MgSO₄.7H₂O, 0.5 g/L Tris(hydroxylmethyl) aminomethane, trace minerals, biotin, vitamins B₁ andB₁₂) and then subsequently isolated to agar plates comprising C mediumsupplemented with phleomycin. As reported by Abe, propagation ofClosterium peracerosum-strigosum-littorals complex in liquid culture wasperformed in C medium. Additional liquid culture medium suitable forpropagation of Closterium peracerosum-strigosum-littorale complex arediscussed by Sekimoto et al., DNA Research, 10:4 (2003), pp. 147-153.Abe reported that the pSA106 plasmid and promoter and 3′ UTR of theClosterium peracerosum-strigosum-littorals complex CAB gene are suitableto enable heterologous gene expression in Closteriumperacerosum-strigosum-littorals complex. In addition, Abe reported thatthe bleomycin resistance cassette encoded on pSA106 was suitable for useas a selectable marker in Closterium peracerosum-strigosum-littoralscomplex. Additional plasmids, promoters, 3′UTR/terminators, andselectable markers suitable for enabling heterologous gene expression inClosterium peracerosum-strigosum-littorale complex have been reported(see Abe et al., Plant Cell Physiology, Vol. 49 (2008), pp. 625-632).

In an embodiment of the present invention, vector pSA106, comprising thenucleotide sequence encoding the ble gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Closteriumperacerosum-strigosum-littorale complex to reflect the codon biasinherent in nuclear genes of Closterium peracerosum-strigosum-littoralecomplex in accordance with Tables 19A-D. For each lipid biosynthesispathway protein of Table 20, the codon-optimized gene sequence canindividually be operably linked to the Closteriumperacerosum-strigosum-littorale complex CAB gene promoter upstream ofthe protein-coding sequence and operably linked to the Closteriumperacerosum-strigosum-littorale complex CAB gene 3′UTR/terminator at the3′ region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Closterium peracerosum-strigosum-littorale complex genome fortargeted genomic integration of the transformation vector. Homologyregions may be selected to disrupt one or more genomic sites ofendogenous lipid biosynthesis pathway genes. Stable transformation ofClosterium peracerosum-strigosum-littorale complex with thetransformation vector is achieved through well-known transformationtechniques including microprojectile bombardment or other known methods.Activity of the ble gene product can be used as a marker to select forClosterium peracerosum-strigosum-littorale complex transformed with thetransformation vector on, but not limited to, C medium comprisingphleomycin. Growth media suitable for Closteriumperacerosum-strigosum-littorale complex lipid production include, butare not limited to C medium and those culture media reported by Abe etal. and Sekimoto et al. Evaluation of fatty acid profiles of Closteriumperacerosum-strigosum-littorale complex lipids can be assessed throughstandard lipid extraction and analytical methods described herein.

Example 18 Engineering Dunaliella Viridis

Expression of recombinant genes in accordance with the present inventionin Dunaliella viridis can be accomplished by modifying the methods andvectors taught by Sun et al. as discussed herein. Briefly, Sun et al.,Gene, Vol. 377 (2006), pp. 140-149, reported the stable transformationof Dunaliella viridis with plasmid DNA. Using the transformation methodof electroporation, Sun introduced the plasmid pDVNR, encoding the fullDunaliella viridis nitrate reductase gene into mutant Dunaliella viridis(Dunaliella viridis NR-mutants.) The NR-mutants are incapable of growthwithout the use of nitrate as a source of nitrogen. Nitrate reductasecatalyzes the conversion of nitrate to nitrite. Prior to transformation,Dunaliella viridis NR-mutants were unable to propagate in culture mediumcomprising nitrate (NO₃ ⁻ 1 ) as the sole nitrogen source. Theexpression of the Dunaliella viridis NR gene product in NR-mutantDunaliella viridis was used as a selectable marker to rescue the nitratemetabolism deficiency. Upon transformation with the pDVNR plasmid,NR-mutant Dunaliella viridis stably expressing the Dunaliella viridis NRgene product were obtained that were able to grow on agar platescomprising nitrate as the sole carbon source. Evaluation of the DNA ofthe stable transformants was performed by Southern analysis. Selectionand maintenance of the transformed Dunaliella viridis (NR mutant) wasperformed on agar plates comprising 5 mM KNO₃. Sun also reported thepropagation of Dunaliella viridis and Dunaliella viridis NR mutants inliquid culture medium. Additional media suitable for propagation ofDunaliella viridis are reported by Gordillo et al., Journal of AppliedPhycology, Vol. 10:2 (1998), pp. 135-144 and by Moulton and Burford,Hydrobiologia, Vols. 204-205:1 (1990), pp. 401-408. Sun reported thatthe plasmid pDVNR and the promoter and 3′ UTR/terminator of theDunaliella viridis nitrate reductase gene were suitable to enableheterologous expression in Dunaliella viridis NR-mutants. Sun alsoreported that expression of the Dunaliella viridis nitrate reductasegene product was suitable for use as a selectable marker in Dunaliellaviridis NR-mutants.

In an embodiment of the present invention, vector pDVNR, comprising thenucleotide sequence encoding the Dunaliella viridis nitrate reductase(DvNR) gene product for use as a selectable marker, is constructed andmodified to further comprise a lipid biosynthesis pathway expressioncassette sequence, thereby creating a transformation vector. The lipidbiosynthesis pathway expression cassette encodes one or more lipidbiosynthesis pathway proteins selected Table 20, each protein-codingsequence codon-optimized for expression in Dunaliella viridis to reflectthe codon bias inherent in nuclear genes of Dunaliella viridis inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the DvNR promoter upstream of the protein-codingsequence and operably linked to the DvNR 3′UTR/terminator at the 3′region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Dunaliella viridis genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Dunaliella viridis NR mutants with thetransformation vector is achieved through well-known transformationtechniques including electroporation or other known methods. Activity ofthe DvNR gene product can be used as a selectable marker to rescue thenitrogen assimilation deficiency of Dunaliella viridis NR mutant strainsand to select for Dunaliella viridis NR-mutants stably expressing thetransformation vector. Growth media suitable for Dunaliella viridislipid production include, but are not limited to those discussed by Sunet al., Moulton and Burford, and Gordillo et al. Evaluation of fattyacid profiles of Dunaliella viridis lipids can be assessed throughstandard lipid extraction and analytical methods described herein.

Example 19 Engineering Dunaliella Salina

Expression of recombinant genes in accordance with the present inventionin Dunaliella salina can be accomplished by modifying the methods andvectors taught by Geng et al. as discussed herein. Briefly, Geng et al.,Journal of Applied Phycology, Vol. 15 (2003), pp. 451-456, reported thestable transformation of Dunaliella salina with plasmid DNA. Using thetransformation method of electroporation, Geng introduced thepUΩHBsAg-CAT plasmid into Dunaliella salina. pUΩHBsAg-CAT comprises ahepatitis B surface antigen (HBsAG) expression cassette comprisingsequence encoding the hepatitis B surface antigen operably linked to aZea mays ubil promoter upstream of the HBsAG protein-coding region andoperably linked to the 3′UTR/terminator of the Agrobacterium tumefaciensnopaline synthase gene (nos) downstream of the HBsAG protein-codingregion. pUΩHBsAg-CAT further comprised a chloramphenicol resistancecassette, comprising sequence encoding the chloramphenicolacetyltransferase (CAT) gene product, conferring resistance to theantibiotic chloramphenicol, operably linked to the simian virus 40promoter and enhancer. Prior to transformation with pUΩHBsAg-CAT,Dunaliella salina was unable to propagate on medium comprising 60 mg/Lchloramphenicol. Upon transformation with the pUΩHBsAg-CAT plasmid,transformants of Dunaliella salina were obtained that were propagated inselective culture medium comprising 60 mg/L chloramphenicol. Theexpression of the CAT gene product in Dunaliella salina enabledpropagation in the presence of 60 mg/L chloramphenicol, therebyestablishing the utility of the chloramphenicol resistance cassette asselectable marker for use in Dunaliella salina. Detectable activity ofthe HBsAg gene product indicated that ubil promoter and nos3′UTR/terminator are suitable for enabling gene expression in Dunaliellasalina. Evaluation of the genomic DNA of the stable transformants wasperformed by Southern analysis. Geng reported that selection andmaintenance of the transformed Dunaliella salina was performed on agarplates comprising Johnson's medium (J1, described by Borowitzka andBorowitzka (eds), Micro-algal Biotechnology. Cambridge University Press,Cambridge, pp. 460-461) with 60 mg/L chloramphenicol. Liquid propagationof Dunaliella salina was performed by Geng in J1 medium with 60 mg/Lchloramphenicol. Propagation of Dunaliella salina in media other than J1medium has been discussed (see Feng et al., Mol. Bio. Reports, Vol. 36(2009), pp. 1433-1439 and Borowitzka et al., Hydrobiologia, Vols.116-117:1 (1984), pp. 115-121). Additional plasmids, promoters,3′UTR/terminators, and selectable markers suitable for enablingheterologous gene expression in Dunaliella salina have been reported byFeng et al. Geng reported that the plasmid pUΩHBsAg-CAT, the ubilpromoter, and the Agrobacterium tumefaciens nopaline synthase gene3′UTR/terminator are suitable to enable exogenous gene expression inDunaliella salina. In addition, Geng reported that the CAT resistancecassette encoded on pUΩHBsAg-CAT was suitable for use as a selectablemarker in Dunaliella salina.

In an embodiment of the present invention, vector pUΩHBsAg-CAT,comprising the nucleotide sequence encoding the CAT gene product for useas a selectable marker, is constructed and modified to further comprisea lipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected Table 20, each protein-coding sequence codon-optimizedfor expression in Dunaliella salina to reflect the codon bias inherentin nuclear genes of Dunaliella salina in accordance with Tables 19A-D.For each lipid biosynthesis pathway protein of Table 20, thecodon-optimized gene sequence can individually be operably linked to theubil promoter upstream of the protein-coding sequence and operablylinked to the Agrobacterium tumefaciens nopaline synthase gene3′UTR/terminator at the 3′ region, or downstream, of the protein-codingsequence. The transformation construct may additionally comprisehomology regions to the Dunaliella salina genome for targeted genomicintegration of the transformation vector. Homology regions may beselected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. Stable transformation of Dunaliella salinawith the transformation vector is achieved through well-knowntransformation techniques including electroporation or other knownmethods. Activity of the CAT gene product can be used as a selectablemarker to select for Dunaliella salina transformed with thetransformation vector in, but not limited to, J1 medium comprisingchloramphenicol. Growth medium suitable for Dunaliella salina lipidproduction include, but are not limited to J1 medium and those culturemedia described by Feng et al. and Borowitzka et al. Evaluation of fattyacid profiles of Dunaliella salina lipids can be assessed throughstandard lipid extraction and analytical methods described herein.

Example 20 Engineering Gonium Pectoral

Expression of recombinant genes in accordance with the present inventionin Gonium pectoral can be accomplished by modifying the methods andvectors taught by Lerche and Hallman et al. as discussed herein.Briefly, Lerche and Hallman et al., BMC Biotechnology, Volume 9:64,2009, reported the stable nuclear transformation of Gonium pectoralewith plasmid DNA. Using the transformation method of microprojectilebombardment, Lerche introduced the plasmid pPmr3 into Gonium pectorale.Plasmid pPmr3 comprised a paromomycin resistance cassette, comprising asequence encoding the aminoglycoside 3′-phosphotransferase (aphVIII)gene product (GenBank Accession No. AAB03856) of Streptomyces rimosusfor resistance to the antibiotic paromomycin, operably linked to theVolvox carteri hsp70A-rbcS3 hybrid promoter upstream of the aphVIIIprotein-coding region and operably linked to the 3′ UTR/terminator ofthe Volvox carteri rbcS3 gene downstream of the aphVIII protein-codingregion. Prior to transformation with pPmr3, Gonium pectorale was unableto propagate on medium comprising 0.06 ug/ml paromomycin. Upontransformation with pPmr3, transformants of Gonium pectorale wereobtained that were propagated in selective culture medium comprising0.75 and greater ug/ml paromomycin. The expression of the aphVIII geneproduct in Gonium pectorale enabled propagation in the presence of 0.75and greater ug/ml paromomycin, thereby establishing the utility of theparomomycin antibiotic resistance cassette as selectable marker for usein Gonium pectorals. Evaluation of the genomic DNA of the stabletransformants was performed by Southern analysis. Lerche and Hallmanreported that selection and maintenance of the transformed Goniumpectorale was performed in liquid Jaworski's medium (20 mg/LCa(NO₃)₂.4H₂O, 12.4 mg/L KH₂PO₄, 50 mg/L MgSO₄.7H₂O, 15.9 mg/L NaHCO₃,2.25 mg/L EDTA-FeNa, 2.25 mg/L EDTA Na₂, 2.48 g/L H₃BO₃, 1.39 g/LMnCl₂.4H₂O, 1 mg/L (NH₄)₆MO₇O₂4.4H₂O, 0.04 mg/L vitamin B12, 0.04 mg/LThiamine-HCl, 0.04 mg/L biotin, 80 mg/L NaNO₃, 36 mg/L Na₄HPO₄.12H₂O)with 1.0 ug/ml paromomycin. Additional plasmids, promoters,3′UTR/terminators, and selectable markers suitable for enablingheterologous gene expression in Gonium pectorale are further discussedby Lerche and Hallman. Lerche and Hallman reported that the plasmidpPmr3, Volvox carteri hsp70A-rbcS3 hybrid promoter, and the 3′UTR/terminator of the Volvox carteri rbcS3 gene are suitable to enableexogenous gene expression in Gonium pectorals. In addition, Lerche andHallman reported that the paromomycin resistance cassette encoded pPmr3was suitable for use as a selectable marker in Gonium pectorale

In an embodiment of the present invention, vector pPmr3, comprising thenucleotide sequence encoding the aphVIII gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected Table 20, each protein-coding sequence codon-optimizedfor expression in Gonium pectorale to reflect the codon bias inherent innuclear genes of Gonium pectorale in accordance with Tables 19A-D. Foreach lipid biosynthesis pathway protein of Table 20, the codon-optimizedgene sequence can individually be operably linked to the Volvox carterihsp70A-rbcS3 hybrid promoter upstream of the protein-coding sequence andoperably linked to the Volvox carteri rbcS3 gene 3′UTR/terminator at the3′ region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Gonium pectorale genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Gonium pectorale with the transformation vectorcan be achieved through well-known transformation techniques includingmicroprojectile bombardment or other known methods. Activity of theaphVIII gene product can be used as a selectable marker to select forGonium pectorale transformed with the transformation vector in, but notlimited to, Jaworski's medium comprising paromomycin. Growth mediasuitable for Gonium pectorale lipid production include Jaworski's mediumand media reported by Stein, American Journal of Botany, Vol. 45:9(1958), pp. 664-672. Evaluation of fatty acid profiles of Goniumpectorale lipids can be assessed through standard lipid extraction andanalytical methods described herein.

Example 21 Engineering Phaeodactylum Tricornutum

Expression of recombinant genes in accordance with the present inventionin Phaeodactylum tricornutum can be accomplished by modifying themethods and vectors taught by Apt et al. as discussed herein. Briefly,Apt et al., Molecular and General Genetics, Vol. 252 (1996), pp.572-579, reported the stable nuclear transformation of Phaeodactylumtricornutum with vector DNA. Using the transformation technique ofmicroprojectile bombardment, Apt introduced the plasmid pfcpA intoPhaeodactylum tricornutum. Plasmid pfcpA comprised a bleomycinresistance cassette, comprising sequence encoding the Streptoalloteichushindustanus Bleomycin binding protein (ble), for resistance to theantibiotics phleomycin and zeocin, operably linked to the promoter ofthe Phaeodactylum tricornutum fucoxanthin chlorophyll a binding proteingene (fcpA) upstream of the ble protein-coding region and operablylinked to the 3′ UTR/terminator of the Phaeodactylum tricornutum fcpAgene at the 3′ region, or downstream of the ble protein-coding region.Prior to transformation with pfcpA, Phaeodactylum tricornutum was unableto propagate on medium comprising 50 ug/ml zeocin. Upon transformationwith pfcpA, transformants of Phaeodactylum tricornutum were obtainedthat were propagated in selective culture medium comprising 50 ug/mlzeocin. The expression of the ble gene product in Phaeodactylumtricornutum enabled propagation in the presence of 50 ug/ml zeocin,thereby establishing the utility of the bleomycin antibiotic resistancecassette as selectable marker for use in Phaeodactylum tricornutum.Evaluation of the genomic DNA of the stable transformants was performedby Southern analysis. Apt reported that selection and maintenance of thetransformed Phaeodactylum tricornutum was performed on agar platescomprising LDM medium (as reported by Starr and Zeikus, Journal ofPhycology, Vol. 29, Supplement, (1993)) with 50 mg/L zeocin. Aptreported liquid propagation of Phaeodactylum tricornutum transformantsin LDM medium with 50 mg/L zeocin. Propagation of Phaeodactylumtricornutum in medium other than LDM medium has been discussed (byZaslayskaia et al., Science, Vol. 292 (2001), pp. 2073-2075, and byRadokovits et al., Metabolic Engineering, Vol. 13 (2011), pp. 89-95).Additional plasmids, promoters, 3′UTR/terminators, and selectablemarkers suitable for enabling heterologous gene expression inPhaeodactylum tricornutum have been reported in the same report by Aptet al., by Zaslayskaia et al., and by Radokovits et al.). Apt reportedthat the plasmid pfcpA, and the Phaeodactylum tricornutum fcpA promoterand 3′ UTR/terminator are suitable to enable exogenous gene expressionin Phaeodactylum tricornutum. In addition, Apt reported that thebleomycin resistance cassette encoded on pfcpA was suitable for use as aselectable marker in Phaeodactylum tricornutum.

In an embodiment of the present invention, vector pfcpA, comprising thenucleotide sequence encoding the ble gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected Table 20, each protein-coding sequence codon-optimizedfor expression in Phaeodactylum tricornutum to reflect the codon biasinherent in nuclear genes of Phaeodactylum tricornutum in accordancewith Tables 19A-D. For each lipid biosynthesis pathway protein of Table20, the codon-optimized gene sequence can individually be operablylinked to the Phaeodactylum tricornutum fcpA gene promoter upstream ofthe protein-coding sequence and operably linked to the Phaeodactylumtricornutum fcpA gene 3′UTR/terminator at the 3′ region, or downstream,of the protein-coding sequence. The transformation construct mayadditionally comprise homology regions to the Phaeodactylum tricornutumgenome for targeted genomic integration of the transformation vector.Homology regions may be selected to disrupt one or more genomic sites ofendogenous lipid biosynthesis pathway genes. One skilled in the art canidentify such homology regions within the sequence of the Phaeodactylumtricornutum genome (referenced in the publication by Bowler et al.,Nature, Vol. 456 (2008), pp. 239-244). Stable transformation ofPhaeodactylum tricornutum with the transformation vector is achievedthrough well-known transformation techniques including microprojectilebombardment or other known methods. Activity of the ble gene product canbe used as a marker to select for Phaeodactylum tricornutum transformedwith the transformation vector in, but not limited to, LDM mediumcomprising paromomycin. Growth medium suitable for Phaeodactylumtricornutum lipid production include, but are not limited to f/2 mediumas reported by Radokovits et al. Evaluation of fatty acid profiles ofPhaeodactylum tricornutum lipids can be assessed through standard lipidextraction and analytical methods described herein.

Example 22 Engineering Chaetoceros sp.

Expression of recombinant genes in accordance with the present inventionin Chaetoceros sp. can be accomplished by modifying the methods andvectors taught by Yamaguchi et al. as discussed herein. Briefly,Yamaguchi et al., Phsycological Research, Vol. 59:2 (2011), pp. 113-119,reported the stable nuclear transformation of Chaetoceros sp. withplasmid DNA. Using the transformation method of microprojectilebombardment, Yamaguchi introduced the plasmid pTpfcp/nat intoChaetoceros sp. pTpfcp/nat comprised a nourseothricin resistancecassette, comprising sequence encoding the nourseothricinacetyltransferase (nat) gene product (GenBank Accession No. AAC60439)operably linked to the Thalassiosira pseudonana fucoxanthin chlorophylla/c binding protein gene (fcp) promoter upstream of the natprotein-coding region and operably linked to the Thalassiosirapseudonana fcp gene 3′ UTR/terminator at the 3′ region (downstream ofthe nat protein coding-sequence). The nat gene product confersresistance to the antibiotic nourseothricin. Prior to transformationwith pTpfcp/nat, Chaetoceros sp. was unable to propagate on mediumcomprising 500 ug/ml nourseothricin. Upon transformation withpTpfcp/nat, transformants of Chaetoceros sp. were obtained that werepropagated in selective culture medium comprising 500 ug/mlnourseothricin. The expression of the nat gene product in Chaetocerossp. enabled propagation in the presence of 500 ug/ml nourseothricin,thereby establishing the utility of the nourseothricin antibioticresistance cassette as selectable marker for use in Chaetoceros sp.Evaluation of the genomic DNA of the stable transformants was performedby Southern analysis. Yamaguchi reported that selection and maintenanceof the transformed Chaetoceros sp. was performed on agar platescomprising f/2 medium (as reported by Guilard, R. R., Culture ofPhytoplankton for feeding marine invertebrates, In Culture of MarineInvertebrate Animals, Smith and Chanley (eds) 1975, Plenum Press, NewYork, pp. 26-60) with 500 ug/ml nourseothricin. Liquid propagation ofChaetoceros sp. transformants, as performed by Yamaguchi, was carriedout in f/2 medium with 500 mg/L nourseothricin. Propagation ofChaetoceros sp. in additional culture medium has been reported (forexample in Napolitano et al., Journal of the World Aquaculture Society,Vol. 21:2 (1990), pp. 122-130, and by Volkman et al., Journal ofExperimental Marine Biology and Ecology, Vol. 128:3 (1989), pp.219-240). Additional plasmids, promoters, 3′UTR/terminators, andselectable markers suitable for enabling heterologous gene expression inChaetoceros sp. have been reported in the same report by Yamaguchi etal. Yamaguchi reported that the plasmid pTpfcp/nat, and theThalassiosira pseudonana fcp promoter and 3′ UTR/terminator are suitableto enable exogenous gene expression in Chaetoceros sp. In addition,Yamaguchi reported that the nourseothricin resistance cassette encodedon pTpfcp/nat was suitable for use as a selectable marker in Chaetocerossp.

In an embodiment of the present invention, vector pTpfcp/nat, comprisingthe nucleotide sequence encoding the nat gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in the closely-related Chaetoceroscompressum to reflect the codon bias inherent in nuclear genes ofChaetoceros compressum in accordance with Tables 19A-D. For each lipidbiosynthesis pathway protein of Table 20, the codon-optimized genesequence can individually be operably linked to the Thalassiosirapseudonana fcp gene promoter upstream of the protein-coding sequence andoperably linked to the Thalassiosira pseudonana fcp gene3′UTR/terminator at the 3′ region, or downstream, of the protein-codingsequence. The transformation construct may additionally comprisehomology regions to the Chaetoceros sp. genome for targeted genomicintegration of the transformation vector. Homology regions may beselected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. Stable transformation of Chaetoceros sp.with the transformation vector is achieved through well-knowntransformation including microprojectile bombardment or other knownmethods. Activity of the nat gene product can be used as a selectablemarker to select for Chaetoceros sp. transformed with the transformationvector in, but not limited to, f/2 agar medium comprisingnourseothricin. Growth medium suitable for Chaetoceros sp. lipidproduction include, but are not limited to, f/2 medium, and thoseculture media discussed by Napolitano et al. and Volkman et al.Evaluation of fatty acid profiles of Chaetoceros sp lipids can beassessed through standard lipid extraction and analytical methodsdescribed herein.

Example 23 Engineering Cylindrotheca Fusiformis

Expression of recombinant genes in accordance with the present inventionin Cylindrotheca fusiformis can be accomplished by modifying the methodsand vectors taught by Poulsen and Kroger et al. as discussed herein.Briefly, Poulsen and Kroger et al., FEBS Journal, Vol. 272 (2005), pp.3413-3423, reported the transformation of Cylindrotheca fusiformis withplasmid DNA. Using the transformation method of microprojectilebombardment, Poulsen and Kroger introduced the pCF-ble plasmid intoCylindrotheca fusiformis. Plasmid pCF-ble comprised a bleomycinresistance cassette, comprising sequence encoding the Streptoalloteichushindustanus Bleomycin binding protein (ble), for resistance to theantibiotics zeocin and phleomycin, operably linked to the Cylindrothecafusiformis fucozanthin chlorophyll a/c binding protein gene (fcpA,GenBank Accession No. AY125580) promoter upstream of the bleprotein-coding region and operably linked to the Cylindrothecafusiformis fcpA gene 3′UTR/terminator at the 3′ region (down-stream ofthe ble protein-coding region). Prior to transformation with pCF-ble,Cylindrotheca fusiformis was unable to propagate on medium comprising 1mg/ml zeocin. Upon transformation with pCF-ble, transformants ofCylindrotheca fusiformis were obtained that were propagated in selectiveculture medium comprising 1 mg/ml zeocin. The expression of the ble geneproduct in Cylindrotheca fusiformis enabled propagation in the presenceof 1 mg/ml zeocin, thereby establishing the utility of the bleomycinantibiotic resistance cassette as selectable marker for use inCylindrotheca fusiformis. Poulsen and Kroger reported that selection andmaintenance of the transformed Cylindrotheca fusiformis was performed onagar plates comprising artificial seawater medium with 1 mg/ml zeocin.Poulsen and Kroger reported liquid propagation of Cylindrothecafusiformis transformants in artificial seawater medium with 1 mg/mlzeocin. Propagation of Cylindrotheca fusiformis in additional culturemedium has been discussed (for example in Liang et al., Journal ofApplied Phycology, Vol. 17:1 (2005), pp. 61-65, and by Orcutt andPatterson, Lipids, Vol. 9:12 (1974), pp. 1000-1003). Additionalplasmids, promoters, and 3′UTR/terminators for enabling heterologousgene expression in Chaetoceros sp. have been reported in the same reportby Poulsen and Kroger. Poulsen and Kroger reported that the plasmidpCF-ble and the Cylindrotheca fusiformis fcp promoter and 3′UTR/terminator are suitable to enable exogenous gene expression inCylindrotheca fusiformis. In addition, Poulsen and Kroger reported thatthe bleomycin resistance cassette encoded on pCF-ble was suitable foruse as a selectable marker in Cylindrotheca fusiformis.

In an embodiment of the present invention, vector pCF-ble, comprisingthe nucleotide sequence encoding the ble gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected Table 20, each protein-coding sequence codon-optimizedfor expression in Cylindrotheca fusiformis to reflect the codon biasinherent in nuclear genes of Cylindrotheca fusiformis in accordance withTables 19A-D. For each lipid biosynthesis pathway protein of Table 20,the codon-optimized gene sequence can individually be operably linked tothe Cylindrotheca fusiformis fcp gene promoter upstream of theprotein-coding sequence and operably linked to the Cylindrothecafusiformis fcp gene 3′UTR/terminator at the 3′ region, or downstream, ofthe protein-coding sequence. The transformation construct mayadditionally comprise homology regions to the Cylindrotheca fusiformisgenome for targeted genomic integration of the transformation vector.Homology regions may be selected to disrupt one or more genomic sites ofendogenous lipid biosynthesis pathway genes. Stable transformation ofCylindrotheca fusiformis with the transformation vector is achievedthrough well-known transformation techniques including microprojectilebombardment or other known methods. Activity of the ble gene product canbe used as a selectable marker to select for Cylindrotheca fusiformistransformed with the transformation vector in, but not limited to,artificial seawater agar medium comprising zeocin. Growth media suitablefor Cylindrotheca fusiformis lipid production include, but are notlimited to, artificial seawater and those media reported by Liang et al.and Orcutt and Patterson. Evaluation of fatty acid profiles ofCylindrotheca fusiformis lipids can be assessed through standard lipidextraction and analytical methods described herein.

Example 24 Engineering Amphidinium sp.

Expression of recombinant genes in accordance with the present inventionin Amphidinium sp. can be accomplished by modifying the methods andvectors taught by ten Lohuis and Miller et al. as discussed herein.Briefly, ten Lohuis and Miller et al., The Plant Journal, Vol. 13:3(1998), pp. 427-435, reported the stable transformation of Amphidiniumsp. with plasmid DNA. Using the transformation technique of agitation inthe presence of silicon carbide whiskers, ten Lohuis introduced theplasmid pMT NPT/GUS into Amphidinium sp. pMT NPT/GUS comprised aneomycin resistance cassette, comprising sequence encoding the neomycinphosphotransferase II (nptII) gene product (GenBank Accession No.AAL92039) operably linked to the Agrobacterium tumefaciens nopalinesynthase (nos) gene promoter upstream, or 5′ of the nptII protein-codingregion and operably linked to the 3′ UTR/terminator of the nos gene atthe 3′ region (down-stream of the nptII protein-coding region). ThenptII gene product confers resistance to the antibiotic G418. The pMTNPT/GUS plasmid further comprised sequence encoding a beta-glucuronidase(GUS) reporter gene product operably-linked to a CaMV 35S promoter andfurther operably linked to the CaMV 35S 3′ UTR/terminator. Prior totransformation with pMT NPT/GUS, Amphidinium sp. was unable to bepropagated on medium comprising 3 mg/ml G418. Upon transformation withpMT NPT/GUS, transformants of Amphidinium sp. were obtained that werepropagated in selective culture medium comprising 3 mg/ml G418. Theexpression of the nptII gene product in Amphidinium sp. enabledpropagation in the presence of 3 mg/ml G418, thereby establishing theutility of the neomycin antibiotic resistance cassette as selectablemarker for use in Amphidinium sp. Detectable activity of the GUSreporter gene indicated that CaMV 35S promoter and 3′UTR are suitablefor enabling gene expression in Amphidinium sp. Evaluation of thegenomic DNA of the stable transformants was performed by Southernanalysis. ten Lohuis and Miller reported liquid propagation ofAmphidinium sp transformants in medium comprising seawater supplementedwith F/2 enrichment solution (provided by the supplier Sigma) and 3mg/ml G418 as well as selection and maintenance of Amphidinium sp.transformants on agar medium comprising seawater supplemented with F/2enrichment solution and 3 mg/ml G418. Propagation of Amphidinium sp. inadditional culture medium has been reported (for example in Mansour etal., Journal of Applied Phycology, Vol. 17:4 (2005) pp. 287-v300). Anadditional plasmid, comprising additional promoters, 3′UTR/terminators,and a selectable marker for enabling heterologous gene expression inAmphidinium sp. have been reported in the same report by ten Lohuis andMiller. ten Lohuis and Miller reported that the plasmid pMT NPT/GUS andthe promoter and 3′ UTR/terminator of the nos and CaMV 35S genes aresuitable to enable exogenous gene expression in Amphidinium sp. Inaddition, ten Lohuis and Miller reported that the neomycin resistancecassette encoded on pMT NPT/GUS was suitable for use as a selectablemarker in Amphidinium sp.

In an embodiment of the present invention, vector pMT NPT/GUS,comprising the nucleotide sequence encoding the nptII gene product foruse as a selectable marker, is constructed and modified to furthercomprise a lipid biosynthesis pathway expression cassette sequence,thereby creating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Amphidinium sp. to reflect the codonbias inherent in nuclear genes of the closely-related species,Amphidinium carterae in accordance with Tables 19A-D. For each lipidbiosynthesis pathway protein of Table 20, the codon-optimized genesequence can individually be operably linked to the Agrobacteriumtumefaciens nopaline synthase (nos) gene promoter upstream of theprotein-coding sequence and operably linked to the nos 3′UTR/terminatorat the 3′ region, or downstream, of the protein-coding sequence. Thetransformation construct may additionally comprise homology regions tothe Amphidinium sp. genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Amphidinium sp. with the transformation vectoris achieved through well-known transformation techniques includingsilicon fibre-mediated microinjection or other known methods. Activityof the nptII gene product can be used as a selectable marker to selectfor Amphidinium sp. transformed with the transformation vector in, butnot limited to, seawater agar medium comprising G418. Growth mediasuitable for Amphidinium sp. lipid production include, but are notlimited to, artificial seawater and those media reported by Mansour etal. and ten Lohuis and Miller. Evaluation of fatty acid profiles ofAmphidinium sp. lipids can be assessed through standard lipid extractionand analytical methods described herein.

Example 25 Engineering Symbiodinium Microadriacticum

Expression of recombinant genes in accordance with the present inventionin Symbiodinium microadriacticum can be accomplished by modifying themethods and vectors taught by ten Lohuis and Miller et al. as discussedherein. Briefly, ten Lohuis and Miller et al., The Plant Journal, Vol.13:3 (1998), pp. 427-435, reported the stable transformation ofSymbiodinium microadriacticum with plasmid DNA. Using the transformationtechnique of silicon fibre-mediated microinjection, ten Lohuisintroduced the plasmid pMT NPT/GUS into Symbiodinium microadriacticum.pMT NPT/GUS comprised a neomycin resistance cassette, comprisingsequence encoding the neomycin phosphotransferase II (nptII) geneproduct (GenBank Accession No. AAL92039) operably linked to theAgrobacterium tumefaciens nopaline synthase (nos) gene promoterupstream, or 5′ of the nptII protein-coding region and operably linkedto the 3′ UTR/terminator of the nos gene at the 3′ region (down-streamof the nptII protein-coding region). The nptII gene product confersresistance to the antibiotic G418. The pMT NPT/GUS plasmid furthercomprised sequence encoding a beta-glucuronidase (GUS) reporter geneproduct operably-linked to a CaMV 35S promoter and further operablylinked to the CaMV 35S 3′ UTR/terminator. Prior to transformation withpMT NPT/GUS, Symbiodinium microadriacticum was unable to be propagatedon medium comprising 3 mg/ml G418. Upon transformation with pMT NPT/GUS,transformants of Symbiodinium microadriacticum were obtained that werepropagated in selective culture medium comprising 3 mg/ml G418. Theexpression of the nptII gene product in Symbiodinium microadriacticumenabled propagation in the presence of 3 mg/ml G418, therebyestablishing the utility of the neomycin antibiotic resistance cassetteas selectable marker for use in Symbiodinium microadriacticum.Detectable activity of the GUS reporter gene indicated that CaMV 35Spromoter and 3′UTR are suitable for enabling gene expression inSymbiodinium microadriacticum. Evaluation of the genomic DNA of thestable transformants was performed by Southern analysis. ten Lohuis andMiller reported liquid propagation of Symbiodinium microadriacticumtransformants in medium comprising seawater supplemented with F/2enrichment solution (provided by the supplier Sigma) and 3 mg/ml G418 aswell as selection and maintenance of Symbiodinium microadriacticumtransformants on agar medium comprising seawater supplemented with F/2enrichment solution and 3 mg/ml G418. Propagation of Symbiodiniummicroadriacticum in additional culture medium has been discussed (forexample in Iglesias-Prieto et al., Proceedings of the National Academyof Sciences, Vol. 89:21 (1992) pp. 10302-10305). An additional plasmid,comprising additional promoters, 3′UTR/terminators, and a selectablemarker for enabling heterologous gene expression in Symbiodiniummicroadriacticum have been discussed in the same report by ten Lohuisand Miller. ten Lohuis and Miller reported that the plasmid pMT NPT/GUSand the promoter and 3′ UTR/terminator of the nos and CaMV 35S genes aresuitable to enable exogenous gene expression in Symbiodiniummicroadriacticum. In addition, ten Lohuis and Miller reported that theneomycin resistance cassette encoded on pMT NPT/GUS was suitable for useas a selectable marker in Symbiodinium microadriacticum.

In an embodiment of the present invention, vector pMT NPT/GUS,comprising the nucleotide sequence encoding the nptII gene product foruse as a selectable marker, is constructed and modified to furthercomprise a lipid biosynthesis pathway expression cassette sequence,thereby creating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected Table 20, each protein-coding sequence codon-optimizedfor expression in Symbiodinium microadriacticum to reflect the codonbias inherent in nuclear genes of Symbiodinium microadriacticum inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Agrobacterium tumefaciens nopaline synthase(nos) gene promoter upstream of the protein-coding sequence and operablylinked to the nos 3′UTR/terminator at the 3′ region, or downstream, ofthe protein-coding sequence. The transformation construct mayadditionally comprise homology regions to the Symbiodiniummicroadriacticum genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Symbiodinium microadriacticum with thetransformation vector is achieved through well-known transformationtechniques including silicon fibre-mediated microinjection or otherknown methods. Activity of the nptII gene product can be used as aselectable marker to select for Symbiodinium microadriacticumtransformed with the transformation vector in, but not limited to,seawater agar medium comprising G418. Growth media suitable forSymbiodinium microadriacticum lipid production include, but are notlimited to, artificial seawater and those media reported byIglesias-Prieto et al. and ten Lohuis and Miller. Evaluation of fattyacid profiles of Symbiodinium microadriacticum lipids can be assessedthrough standard lipid extraction and analytical methods describedherein.

Example 26 Engineering Nannochloropsis sp.

Expression of recombinant genes in accordance with the present inventionin Nannochloropsis sp. W2J3B can be accomplished by modifying themethods and vectors taught by Kilian et al. as discussed herein.Briefly, Kilian et al., Proceedings of the National Academy of Sciences,Vol. 108:52 (2011) pp. 21265-21269, reported the stable nucleartransformation of Nannochloropsis with a transformation construct. Usingthe transformation method of electroporation, Kilian introduced thetransformation construct C2 into Nannochloropsis sp. W2J3B. The C2transformation construct comprised a bleomycin resistance cassette,comprising the coding sequence for the Streptoalloteichus hindustanusBleomycin binding protein (ble), for resistance to the antibioticsphleomycin and zeocin, operably linked to and the promoter of theNannochloropsis sp. W2J3B violaxanthin/chlorophyll a-binding proteingene VCP2 upstream of the ble protein-coding region and operably linkedto the 3′UTR/terminator of the Nannochloropsis sp. W2J3Bviolaxanthin/chlorophyll a-binding gene VCP1 downstream of the bleprotein-coding region. Prior to transformation with C2, Nannochloropsissp. W2J3B was unable to propagate on medium comprising 2 ug/ml zeocin.Upon transformation with C2, transformants of Nannochloropsis sp. W2J3Bwere obtained that were propagated in selective culture mediumcomprising 2 ug/ml zeocin. The expression of the ble gene product inNannochloropsis sp. W2J3B enabled propagation in the presence of 2 ug/mlzeocin, thereby establishing the utility of the bleomycin antibioticresistance cassette as selectable marker for use in Nannochloropsis.Evaluation of the genomic DNA of the stable transformants was performedby PCR. Kilian reported liquid propagation of Nannochloropsis sp. W2J3Btransformants in F/2 medium (reported by Guilard and Ryther, CanadianJournal of Microbiology, Vol. 8 (1962), pp. 229-239) comprising fivefoldlevels of trace metals, vitamins, and phosphate solution, and furthercomprising 2 ug/ml zeocin. Kilian also reported selection andmaintenance of Nannochloropsis sp. W2J3B transformants on agar F/2medium comprising artificial seawater 2 mg/ml zeocin. Propagation ofNannochloropsis in additional culture medium has been discussed (forexample in Chiu et al., Bioresour Technol., Vol. 100:2 (2009), pp.833-838 and Pal et al., Applied Microbiology and Biotechnology, Vol.90:4 (2011), pp. 1429-1441.). Additional transformation constructs,comprising additional promoters and 3′UTR/terminators for enablingheterologous gene expression in Nannochloropsis sp. W2J3B and selectablemarkers for selection of transformants have been described in the samereport by Kilian. Kilian reported that the transformation construct C2and the promoter of the Nannochloropsis sp. W2J3Bviolaxanthin/chlorophyll a-binding protein gene VCP2 and 3′UTR/terminator of the Nannochloropsis sp. W2J3B violaxanthin/chlorophylla-binding protein gene VCP1 are suitable to enable exogenous geneexpression in Nannochloropsis sp. W2J3B. In addition, Kilian reportedthat the bleomycin resistance cassette encoded on C2 was suitable foruse as a selectable marker in Nannochloropsis sp. W2J3B.

In an embodiment of the present invention, transformation construct C2,comprising the nucleotide sequence encoding the ble gene product for useas a selectable marker, is constructed and modified to further comprisea lipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Nannochloropsis sp. W2J3B to reflectthe codon bias inherent in nuclear genes of Nannochloropsis sp. inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Nannochloropsis sp. W2J3B VCP2 gene promoterupstream of the protein-coding sequence and operably linked to theNannochloropsis sp. W2J3B VCP1 gene 3′UTR/terminator at the 3′ region,or downstream, of the protein-coding sequence. The transformationconstruct may additionally comprise homology regions to theNannochloropsis sp. W2J3B genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic sites of endogenous lipid biosynthesis pathway genes.Stable transformation of Nannochloropsis sp. W2J3B with thetransformation vector is achieved through well-known transformationtechniques including electroporation or other known methods. Activity ofthe ble gene product can be used as a selectable marker to select forNannochloropsis sp. W2J3B transformed with the transformation vector in,but not limited to, F/2 medium comprising zeocin. Growth media suitablefor Nannochloropsis sp. W2J3B lipid production include, but are notlimited to, F/2 medium and those media reported by Chiu et al. and Palet al. Evaluation of fatty acid profiles of Nannochloropsis sp. W2J3Blipids can be assessed through standard lipid extraction and analyticalmethods described herein.

Example 27 Engineering Cyclotella Cryptica

Expression of recombinant genes in accordance with the present inventionin Cyclotella cryptica can be accomplished by modifying the methods andvectors taught by Dunahay et al. as discussed herein. Briefly, Dunahayet al., Journal of Phycology, Vol. 31 (1995), pp. 1004-1012, reportedthe stable transformation of Cyclotella cryptica with plasmid DNA. Usingthe transformation method of microprojectile bombardment, Dunahayintroduced the plasmid pACCNPT5.1 into Cyclotella cryptica. PlasmidpACCNPT5.1 comprised a neomycin resistance cassette, comprising thecoding sequence of the neomycin phosphotransferase II (nptII) geneproduct operably linked to the promoter of the Cyclotella crypticaacetyl-CoA carboxylase (ACCase) gene (GenBank Accession No. L20784)upstream of the nptII coding-region and operably linked to the3′UTR/terminator of the Cyclotella cryptica ACCase gene at the 3′ region(downstream of the nptII coding-region). The nptII gene product confersresistance to the antibiotic G418. Prior to transformation withpACCNPT5.1, Cyclotella cryptica was unable to propagate on 50%artificial seawater medium comprising 100 ug/ml G418. Upontransformation with pACCNPT5.1, transformants of Cyclotella crypticawere obtained that were propagated in selective 50% artificial seawatermedium comprising 100 ug/ml G418. The expression of the nptII geneproduct in Cyclotella cryptica enabled propagation in the presence of100 ug/ml G418, thereby establishing the utility of the neomycinantibiotic resistance cassette as selectable marker for use inCyclotella cryptica. Evaluation of the genomic DNA of the stabletransformants was performed by Southern analysis. Dunahay reportedliquid propagation of Cyclotella cryptica in artificial seawater medium(ASW, as discussed by Brown, L., Phycologia, Vol. 21 (1982), pp.408-410) supplemented with 1.07 mM sodium silicate and with 100 ug/mlG418. Dunahay also reported selection and maintenance of Cyclotellacryptica transformants on agar plates comprising ASW medium with 100ug/ml G418. Propagation of Cyclotella cryptica in additional culturemedium has been discussed (for example in Sriharan et al., AppliedBiochemistry and Biotechnology, Vol. 28-29:1 (1991), pp. 317-326 andPahl et al., Journal of Bioscience and Bioengineering, Vol. 109:3(2010), pp. 235-239). Dunahay reported that the plasmid pACCNPT5.1 andthe promoter of the Cyclotella cryptica acetyl-CoA carboxylase (ACCase)gene are suitable to enable exogenous gene expression in Cyclotellacryptica. In addition, Dunahay reported that the neomycin resistancecassette encoded on pACCNPT5.1 was suitable for use as a selectablemarker in Cyclotella cryptica.

In an embodiment of the present invention, vector pACCNPT5.1, comprisingthe nucleotide sequence encoding the nptII gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Cyclotella cryptica to reflect thecodon bias inherent in nuclear genes of Cyclotella cryptica inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Cyclotella cryptica ACCase promoter upstreamof the protein-coding sequence and operably linked to the Cyclotellacryptica ACCase 3′UTR/terminator at the 3′ region, or downstream, of theprotein-coding sequence. The transformation construct may additionallycomprise homology regions to the Cyclotella cryptica genome for targetedgenomic integration of the transformation vector. Homology regions maybe selected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. Stable transformation of Cyclotella crypticawith the transformation vector is achieved through well-knowntransformation techniques including microprojectile bombardment or otherknown methods. Activity of the nptII gene product can be used as amarker to select for Cyclotella cryptica transformed with thetransformation vector in, but not limited to, agar ASW medium comprisingG418. Growth media suitable for Cyclotella cryptica lipid productioninclude, but are not limited to, ASW medium and those media reported bySriharan et al., 1991 and Pahl et al. Evaluation of fatty acid profilesof Cyclotella cryptica lipids can be assessed through standard lipidextraction and analytical methods described herein.

Example 28 Engineering Navicula Saprophila

Expression of recombinant genes in accordance with the present inventionin Navicula saprophila can be accomplished by modifying the methods andvectors taught by Dunahay et al. as discussed herein. Briefly, Dunahayet al., Journal of Phycology, Vol. 31 (1995), pp. 1004-1012, reportedthe stable transformation of Navicula saprophila with plasmid DNA. Usingthe transformation method of microprojectile bombardment, Dunahayintroduced the plasmid pACCNPT5.1 into Navicula saprophila. PlasmidpACCNPT5.1 comprised a neomycin resistance cassette, comprising thecoding sequence of the neomycin phosphotransferase II (nptII) geneproduct operably linked to the promoter of the Cyclotella crypticaacetyl-CoA carboxylase (ACCase) gene (GenBank Accession No. L20784)upstream of the nptII coding-region and operably linked to the3′UTR/terminator of the Cyclotella cryptica ACCase gene at the 3′ region(downstream of the nptII coding-region). The nptII gene product confersresistance to the antibiotic G418. Prior to transformation withpACCNPT5.1, Navicula saprophila was unable to propagate on artificialseawater medium comprising 100 ug/ml G418. Upon transformation withpACCNPT5.1, transformants of Navicula saprophila were obtained that werepropagated in selective artificial seawater medium comprising 100 ug/mlG418. The expression of the nptII gene product in Navicula saprophilaenabled propagation in the presence of G418, thereby establishing theutility of the neomycin antibiotic resistance cassette as selectablemarker for use in Navicula saprophila. Evaluation of the genomic DNA ofthe stable transformants was performed by Southern analysis. Dunahayreported liquid propagation of Navicula saprophila in artificialseawater medium (ASW, as discussed by Brown, L., Phycologia, Vol. 21(1982), pp. 408-410) supplemented with 1.07 mM sodium silicate and with100 ug/ml G418. Dunahay also reported selection and maintenance ofNavicula saprophila transformants on agar plates comprising ASW mediumwith 100 ug/ml G418. Propagation of Navicula saprophila in additionalculture medium has been discussed (for example in Tadros and Johansen,Journal of Phycology, Vol. 24:4 (1988), pp. 445-452 and Sriharan et al.,Applied Biochemistry and Biotechnology, Vol. 20-21:1 (1989), pp.281-291). Dunahay reported that the plasmid pACCNPT5.1 and the promoterof the Cyclotella cryptica acetyl-CoA carboxylase (ACCase) gene aresuitable to enable exogenous gene expression in Navicula saprophila. Inaddition, Dunahay reported that the neomycin resistance cassette encodedon pACCNPT5.1 was suitable for use as a selectable marker in Naviculasaprophila.

In an embodiment of the present invention, vector pACCNPT5.1, comprisingthe nucleotide sequence encoding the nptII gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Navicula saprophila to reflect thecodon bias inherent in nuclear genes of the closely-related Naviculapelliculosa in accordance with Tables 19A-D. For each lipid biosynthesispathway protein of Table 20, the codon-optimized gene sequence canindividually be operably linked to the Cyclotella cryptica ACCase genepromoter upstream of the protein-coding sequence and operably linked tothe Cyclotella cryptica ACCase gene 3′UTR/terminator at the 3′ region,or downstream, of the protein-coding sequence. The transformationconstruct may additionally comprise homology regions to the Naviculasaprophila genome for targeted genomic integration of the transformationvector. Homology regions may be selected to disrupt one or more genomicsites of endogenous lipid biosynthesis pathway genes. Stabletransformation of Navicula saprophila with the transformation vector isachieved through well-known transformation techniques includingmicroprojectile bombardment or other known methods. Activity of thenptII gene product can be used as a selectable marker to select forNavicula saprophila transformed with the transformation vector in, butnot limited to, agar ASW medium comprising G418. Growth media suitablefor Navicula saprophila lipid production include, but are not limitedto, ASW medium and those media reported by Sriharan et al. 1989 andTadros and Johansen. Evaluation of fatty acid profiles of Naviculasaprophila lipids can be assessed through standard lipid extraction andanalytical methods described herein.

Example 29 Engineering Thalassiosira Pseudonana

Expression of recombinant genes in accordance with the present inventionin Thalassiosira pseudonana can be accomplished by modifying the methodsand vectors taught by Poulsen et al. as discussed herein. Briefly,Poulsen et al., Journal of Phycology, Vol. 42 (2006), pp. 1059-1065,reported the stable transformation of Thalassiosira pseudonana withplasmid DNA. Using the transformation method of microprojectilebombardment, Poulsen introduced the plasmid pTpfcp/nat in toThalassiosira pseudonana. pTpfcp/nat comprised a nourseothricinresistance cassette, comprising sequence encoding the nourseothricinacetyltransferase (nat) gene product (GenBank Accession No. AAC60439)operably linked to the Thalassiosira pseudonana fucoxanthin chlorophylla/c binding protein gene (fcp) promoter upstream of the natprotein-coding region and operably linked to the Thalassiosirapseudonana fcp gene 3′ UTR/terminator at the 3′ region (downstream ofthe nat protein coding-sequence). The nat gene product confersresistance to the antibiotic nourseothricin. Prior to transformationwith pTpfcp/nat, Thalassiosira pseudonana was unable to propagate onmedium comprising 10 ug/ml nourseothricin. Upon transformation withpTpfcp/nat, transformants of Thalassiosira pseudonana were obtained thatwere propagated in selective culture medium comprising 100 ug/mlnourseothricin. The expression of the nat gene product in Thalassiosirapseudonana enabled propagation in the presence of 100 ug/mlnourseothricin, thereby establishing the utility of the nourseothricinantibiotic resistance cassette as selectable marker for use inThalassiosira pseudonana. Evaluation of the genomic DNA of the stabletransformants was performed by Southern analysis. Poulsen reported thatselection and maintenance of the transformed Thalassiosira pseudonanawas performed in liquid culture comprising modified ESAW medium (asdiscussed by Harrison et al., Journal of Phycology, Vol. 16 (1980), pp.28-35) with 100 ug/ml nourseothricin. Propagation of Thalassiosirapseudonana in additional culture medium has been discussed (for examplein Volkman et al., Journal of Experimental Marine Biology and Ecology,Vol. 128:3 (1989), pp. 219-240). An additional plasmid, comprisingadditional selectable markers suitable for use in Thalassiosirapseudonana has been discussed in the same report by Poulsen. Poulsenreported that the plasmid pTpfcp/nat, and the Thalassiosira pseudonanafcp promoter and 3′ UTR/terminator are suitable to enable exogenous geneexpression in Thalassiosira pseudonana. In addition, Poulsen reportedthat the nourseothricin resistance cassette encoded on pTpfcp/nat wassuitable for use as a selectable marker in Thalassiosira pseudonana.

In an embodiment of the present invention, vector pTpfcp/nat, comprisingthe nucleotide sequence encoding the nat gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Thalassiosira pseudonana to reflectthe codon bias inherent in nuclear genes of Thalassiosira pseudonana inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Thalassiosira pseudonana fcp gene promoterupstream of the protein-coding sequence and operably linked to theThalassiosira pseudonana fcp gene 3′UTR/terminator at the 3′ region, ordownstream, of the protein-coding sequence. The transformation constructmay additionally comprise homology regions to the Thalassiosirapseudonana genome for targeted genomic integration of the transformationvector. Homology regions may be selected to disrupt one or more genomicsites of endogenous lipid biosynthesis pathway genes. One skilled in theart can identify such homology regions within the sequence of theThalassiosira pseudonana genome (referenced in the publication byArmbrust et al., Science, Vol. 306: 5693 (2004): pp. 79-86). Stabletransformation of Thalassiosira pseudonana with the transformationvector is achieved through well-known transformation techniquesincluding microprojectile bombardment or other known methods. Activityof the nat gene product can be used as a marker to select forThalassiosira pseudonana transformed with the transformation vector inbut not limited to, ESAW agar medium comprising nourseothricin. Growthmedia suitable for Thalassiosira pseudonana lipid production include,but are not limited to, ESAW medium, and those culture media discussedby Volkman et al. and Harrison et al. Evaluation of fatty acid profilesof Thalassiosira pseudonana lipids can be assessed through standardlipid extraction and analytical methods described herein.

Example 30 Engineering Chlamydomonas Reinhardtii

Expression of recombinant genes in accordance with the present inventionin Chlamydomonas reinhardtii can be accomplished by modifying themethods and vectors taught by Cerutti et al. as discussed herein.Briefly, Cerutti et al., Genetics, Vol. 145:1 (1997), pp. 97-110,reported the stable nuclear transformation of Chlamydomonas reinhardtiiwith a transformation vector. Using the transformation method ofmicroprojectile bombardment, Cerutti introduced transformation constructP[1030] into Chlamydomonas reinhardtii. Construct P[1030] comprised aspectinomycin resistance cassette, comprising sequence encoding theaminoglucoside 3″-adenyltransferase (aadA) gene product operably linkedto the Chlamydomonas reinhardtii ribulose-1,5-bisphosphatecarboxylase/oxygenase small subunit gene (RbcS2, GenBank Accession No.X04472) promoter upstream of the aadA protein-coding region and operablylinked to the Chlamydomonas reinhardtii RbcS2 gene 3′ UTR/terminator atthe 3′ region (downstream of the aadA protein coding-sequence). The aadAgene product confers resistance to the antibiotic spectinomycin. Priorto transformation with P[1030], Chlamydomonas reinhardtii was unable topropagate on medium comprising 90 ug/ml spectinomycin. Upontransformation with P[1030], transformants of Chlamydomonas reinhardtiiwere obtained that were propagated in selective culture mediumcomprising 90 ug/ml spectinomycin, thereby establishing the utility ofthe spectinomycin antibiotic resistance cassette as a selectable markerfor use in Chlamydomonas reinhardtii. Evaluation of the genomic DNA ofthe stable transformants was performed by Southern analysis. Ceruttireported that selection and maintenance of the transformed Chlamydomonasreinhardtii was performed on agar plates comprisingTris-acetate-phosphate medium (TAP, as described by Harris, TheChlamydomonas Sourcebook, Academic Press, San Diego, 1989) with 90 ug/mlspectinomycin. Cerutti additionally reported propagation ofChlamydomonas reinhardtii in TAP liquid culture with 90 ug/mlspectinomycin. Propagation of Chlamydomonas reinhardtii in alternativeculture medium has been discussed (for example in Dent et al., AfricanJournal of Microbiology Research, Vol. 5:3 (2011), pp. 260-270 andYantao et al., Biotechnology and Bioengineering, Vol. 107:2 (2010), pp.258-268). Additional constructs, comprising additional selectablemarkers suitable for use in Chlamydomonas reinhardtii as well asnumerous regulatory sequences, including promoters and 3′ UTRs suitablefor promoting heterologous gene expression in Chlamydomonas reinhardtiiare known in the art and have been discussed (for a review, seeRadakovits et al., Eukaryotic Cell, Vol. 9:4 (2010), pp. 486-501).Cerutti reported that the transformation vector P[1030] and theChlamydomonas reinhardtii promoter and 3′ UTR/terminator are suitable toenable exogenous gene expression in Chlamydomonas reinhardtii. Inaddition, Cerutti reported that the spectinomycin resistance cassetteencoded on P[1030] was suitable for use as a selectable marker inChlamydomonas reinhardtii.

In an embodiment of the present invention, vector P[1030], comprisingthe nucleotide sequence encoding the aadA gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Chlamydomonas reinhardtii to reflectthe codon bias inherent in nuclear genes of Chlamydomonas reinhardtii inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Chlamydomonas reinhardtii RbcS2 promoterupstream of the protein-coding sequence and operably linked to theChlamydomonas reinhardtii RbcS2 3′UTR/terminator at the 3′ region, ordownstream, of the protein-coding sequence. The transformation constructmay additionally comprise homology regions to the Chlamydomonasreinhardtii genome for targeted genomic integration of thetransformation vector. Homology regions may be selected to disrupt oneor more genomic site of an endogenous lipid biosynthesis pathway gene.One skilled in the art can identify such homology regions within thesequence of the Chlamydomonas reinhardtii genome (referenced in thepublication by Merchant et al., Science, Vol. 318:5848 (2007), pp.245-250). Stable transformation of Chlamydomonas reinhardtii with thetransformation vector is achieved through well-known transformationtechniques including microprojectile bombardment or other known methods.Activity of the aadA gene product can be used as a marker to select forChlamydomonas reinhardtii transformed with the transformation vector on,but not limited to, TAP agar medium comprising spectinomycin. Growthmedia suitable for Chlamydomonas reinhardtii lipid production include,but are not limited to, ESAW medium, and those culture media discussedby Yantao et al. and Dent et al. Evaluation of fatty acid profiles ofChlamydomonas reinhardtii lipids can be assessed through standard lipidextraction and analytical methods described herein.

Example 31 Engineering Yarrowia Lipolytica

Expression of recombinant genes in accordance with the present inventionin Yarrowia lipolytica can be accomplished by modifying the methods andvectors taught by Fickers et al. as discussed herein. Briefly, Fickerset al., Journal of Microbiological Methods, Vol. 55 (2003), pp. 727-737,reported the stable nuclear transformation of Yarrowia lipolytica withplasmid DNA. Using a lithium acetate transformation method, Fickersintroduced the plasmid JMP123 into Yarrowia lipolytica. Plasmid JMP123comprised a hygromycin B resistance cassette, comprising sequenceencoding the hygromycin B phosphotransferase gene product (hph),operably-linked to the Yarrowia lipolytica LIP2 gene promoter (GenBankAccession No. AJ012632) upstream of the hph protein-coding region andoperably linked to the Yarrowia lipolytica LIP2 gene 3′UTR/terminatordownstream of the hph protein-coding region. Prior to transformationwith JMP123, Yarrowia lipolytica were unable to propagate on mediumcomprising 100 ug/ml hygromycin. Upon transformation with JMP123,transformed Yarrowia lipolytica were obtained that were able topropagate on medium comprising 100 ug/ml hygromycin, therebyestablishing the hygromycin B antibiotic resistance cassette as aselectable marker for use in Yarrowia lipolytica. The nucleotidesequence provided on JMP123 of the promoter and 3′UTR/terminator of theYarrowia lipolytica LIP2 gene served as donor sequences for homologousrecombination of the hph coding sequence into the LIP2 locus. Evaluationof the genomic DNA of the stable transformants was performed bySouthern. Fickers reported that selection and maintenance of thetransformed Yarrowia lipolytica was performed on agar plates comprisingstandard YPD medium (Yeast Extract Peptone Dextrose) with 100 ug/mlhygromycin. Liquid culturing of transformed Yarrowia lipolytica wasperformed in YPD medium with hygromycin. Other media and techniques usedfor culturing Yarrowia lipolytica have been reported and numerous otherplasmids, promoters, 3′ UTRs, and selectable markers for use in Yarrowialipolytica have been reported (for example see Pignede et al., Appliedand Environmental Biology, Vol. 66:8 (2000), pp. 3283-3289, Chuang etal., New Biotechnology, Vol. 27:4 (2010), pp. 277-282, and Barth andGaillardin, (1996), In: K, W. (Ed.), Nonconventional Yeasts inBiotechnology. Sprinter-Verlag, Berlin-Heidelber, pp. 313-388). Fickersreported that the transformation vector JMP 123 and the Yarrowialipolytica LIP2 gene promoter and 3′ UTR/terminator are suitable toenable heterologous gene expression in Yarrowia lipolytica. In addition,Fickers reported that the hygromycin resistance cassette encoded onJMP123 was suitable for use as a selectable marker in Yarrowialipolytica.

In an embodiment of the present invention, vector JMP123, comprising thenucleotide sequence encoding the hph gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Yarrowia lipolytica to reflect thecodon bias inherent in nuclear genes of Yarrowia lipolytica inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the Yarrowia lipolytica LIP2 gene promoterupstream of the protein-coding sequence and operably linked to theYarrowia lipolytica LIP2 gene 3′UTR/terminator at the 3′ region, ordownstream, of the protein-coding sequence. The transformation constructmay additionally comprise homology regions to the Yarrowia lipolyticagenome for targeted genomic integration of the transformation vector.Homology regions may be selected to disrupt one or more genomic sites ofendogenous lipid biosynthesis pathway genes. One skilled in the art canidentify such homology regions within the sequence of the Yarrowialipolytica genome (referenced in the publication by Dujun et al.,Nature, Vol. 430 (2004), pp. 35-44). Stable transformation of Yarrowialipolytica with the transformation vector is achieved through well-knowntransformation techniques including lithium acetate transformation orother known methods. Activity of the hph gene product can be used as amarker to select for Yarrowia lipolytica transformed with thetransformation vector on, but not limited to, YPD medium comprisinghygromycin. Growth media suitable for Yarrowia lipolytica lipidproduction include, but are not limited to, YPD medium, and thoseculture media described by Chuang et al. Evaluation of fatty acidprofiles of Yarrowia lipolytica lipids can be assessed through standardlipid extraction and analytical methods described herein.

Example 32 Engineering Mortierella Alpine

Expression of recombinant genes in accordance with the present inventionin Mortierella alpine can be accomplished by modifying the methods andvectors taught by Mackenzie et al. as discussed herein. Briefly,Mackenzie et al., Applied and Environmental Microbiology, Vol. 66(2000), pp. 4655-4661, reported the stable nuclear transformation ofMortierella alpina with plasmid DNA. Using a protoplast transformationmethod, MacKenzie introduced the plasmid pD4 into Mortierella alpina.Plasmid pD4 comprised a hygromycin B resistance cassette, comprisingsequence encoding the hygromycin B phosphotransferase gene product(hpt), operably-linked to the Mortierella alpina histone H4.1 genepromoter (GenBank Accession No. AJ249812) upstream of the hptprotein-coding region and operably linked to the Aspergillus nidulansN-(5′-phophoribosyl)anthranilate isomerase (trpC) gene 3′UTR/terminatordownstream of the hpt protein-coding region. Prior to transformationwith pD4, Mortierella alpina were unable to propagate on mediumcomprising 300 ug/ml hygromycin. Upon transformation with pD4,transformed Mortierella alpina were obtained that were propagated onmedium comprising 300 ug/ml hygromycin, thereby establishing thehygromycin B antibiotic resistance cassette as a selectable marker foruse in Mortierella alpina. Evaluation of the genomic DNA of the stabletransformants was performed by Southern. Mackenzie reported thatselection and maintenance of the transformed Mortierella alpina wasperformed on PDA (potato dextrose agar) medium comprising hygromycin.Liquid culturing of transformed Mortierella alpina by Mackenzie wasperformed in PDA medium or in S2GYE medium (comprising 5% glucose, 0.5%yeast extract, 0.18% NH₄SO₄, 0.02% MgSO₄-7H₂O, 0.0001% FeCl₃-6H₂O, 0.1%,trace elements, 10 mM K₂HPO₄—NaH₂PO₄), with hygromycin. Other media andtechniques used for culturing Mortierella alpina have been reported andother plasmids, promoters, 3′ UTRs, and selectable markers for use inMortierella alpina have been reported (for example see Ando et al.,Applied and Environmental Biology, Vol. 75:17 (2009) pp. 5529-35 and Luet al., Applied Biochemistry and Biotechnology, Vol. 164:7 (2001), pp.979-90). Mackenzie reported that the transformation vector pD4 and theMortierella alpina histone H4.1 promoter and A. nidulans trpC gene 3′UTR/terminator are suitable to enable heterologous gene expression inMortierella alpina. In addition, Mackenzie reported that the hygromycinresistance cassette encoded on pD4 was suitable for use as a selectablemarker in Mortierella alpina.

In an embodiment of the present invention, vector pD4, comprising thenucleotide sequence encoding the hpt gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Mortierella alpina to reflect thecodon bias inherent in nuclear genes of Mortierella alpina in accordancewith Tables 19A-D. For each lipid biosynthesis pathway protein of Table20, the codon-optimized gene sequence can individually be operablylinked to the Mortierella alpina histone H4.1 gene promoter upstream ofthe protein-coding sequence and operably linked to the A. nidulans trpC3′UTR/terminator at the 3′ region, or downstream, of the protein-codingsequence. The transformation construct may additionally comprisehomology regions to the Mortierella alpina genome for targeted genomicintegration of the transformation vector. Homology regions may beselected to disrupt one or more genomic sites of endogenous lipidbiosynthesis pathway genes. One skilled in the art can identify suchhomology regions within the sequence of the Mortierella alpina genome(referenced in the publication by Wang et al., PLOS One, Vol. 6:12(2011)). Stable transformation of Mortierella alpina with thetransformation vector is achieved through well-known transformationtechniques including protoplast transformation or other known methods.Activity of the hpt gene product can be used as a marker to select forMortierella alpina transformed with the transformation vector on, butnot limited to, PDA medium comprising hygromycin. Growth media suitablefor Mortierella alpina lipid production include, but are not limited to,S2GYE medium, and those culture media described by Lu et al. and Ando etal. Evaluation of fatty acid profiles of Mortierella alpina lipids canbe assessed through standard lipid extraction and analytical methodsdescribed herein.

Example 33 Engineering Rhodococcus Opacus PD630

Expression of recombinant genes in accordance with the present inventionin Rhodococcus opacus PD630 can be accomplished by modifying the methodsand vectors taught by Kalscheuer et al. as discussed herein. Briefly,Kalscheuer et al., Applied and Environmental Microbiology, Vol. 52(1999), pp. 508-515, reported the stable transformation of Rhodococcusopacus with plasmid DNA. Using the transformation method ofelectroporation, Kalscheuer introduced the plasmid pNC9501 intoRhodococcus opacus PD630. Plasmid pNC9501 comprised a thiostreptonresistance (thio^(r)) cassette, comprising the full nucleotide sequenceof the Streptomyces azureus 23S rRNA A1067 methyltransferase gene,including the gene's promoter and 3′ terminator sequence. Prior totransformation with pNC9501, Rhodococcus opacus was unable to propagateon medium comprising 1 mg/ml thiostrepton. Upon transformation ofRhodococcus opacus PD630 with pNC9501, transformants were obtained thatpropagated on culture medium comprising 1 mg/ml thiostrepton, therebyestablishing the use of the thiostrepton resistance cassette as aselectable marker in Rhodococcus opacus PD630. A second plasmiddescribed by Kalscheuer, pAK68, comprised the resistance thio^(r)cassette as well as the gene sequences of the Ralstonia eutrophabeta-ketothiolase (phaB), acetoacetyl-CoA reductase (phaA), andpoly3-hydroxyalkanoic acid synthase (phaC) genes forpolyhydroxyalkanoate biosynthesis, driven by the lacZ promoter. UponpAK68 transformation of a Rhodococcus opacus PD630 strain deficient inpolyhydroxyalkanoate biosynthesis, transformed Rhodococcus opacus PD630were obtained that produced higher amounts of polyhydroxyalkanoates thanthe untransformed strain. Detectable activity of the introducedRalstonia eutropha phaB, phaA, and phaC enzymes indicted that theregulatory elements encoded on the pAK68 plasmid were suitable forheterologous gene expression in Rhodococcus opacus PD630. Kalscheuerreported that selection and maintenance of the transformed Rhodococcusopacus PD630 was performed on standard Luria Broth (LB) medium, nutrientbroth (NB), or mineral salts medium (MSM) comprising thiostrepton. Othermedia and techniques used for culturing Rhodococcus opacus PD630 havebeen described (for example see Kurosawa et al., Journal ofBiotechnology, Vol. 147:3-4 (2010), pp. 212-218 and Alverez et al.,Applied Microbial and Biotechnology, Vol. 54:2 (2000), pp. 218-223).Kalscheuer reported that the transformation vectors pNC9501 and pAK68,the promoters of the Streptomyces azureus 23S rRNA A1067methyltransferase gene and lacZ gene are suitable to enable heterologousgene expression in Rhodococcus opacus PD630. In addition, Kalscheuerreported that the thio^(r) cassette encoded on pNC9501 and pAK68 wassuitable for use as a selectable marker in Rhodococcus opacus PD630.

In an embodiment of the present invention, vector pNC9501, comprisingthe nucleotide sequence encoding the thio^(r) gene product for use as aselectable marker, is constructed and modified to further comprise alipid biosynthesis pathway expression cassette sequence, therebycreating a transformation vector. The lipid biosynthesis pathwayexpression cassette encodes one or more lipid biosynthesis pathwayproteins selected from Table 20, each protein-coding sequencecodon-optimized for expression in Rhodococcus opacus PD630 to reflectthe codon bias inherent in nuclear genes of Rhodococcus opacus inaccordance with Tables 19A-D. For each lipid biosynthesis pathwayprotein of Table 20, the codon-optimized gene sequence can individuallybe operably linked to the lacZ gene promoter upstream of theprotein-coding sequence. The transformation construct may additionallycomprise homology regions to the Rhodococcus opacus PD630 genome fortargeted genomic integration of the transformation vector. Homologyregions may be selected to disrupt one or more genomic sites ofendogenous lipid biosynthesis pathway genes. One skilled in the art canidentify such homology regions within the sequence of the Rhodococcusopacus PD630 genome (referenced in the publication by Holder et al.,PLOS Genetics, Vol. 7:9 (2011). Transformation of Rhodococcus opacusPD630 with the transformation vector is achieved through well-knowntransformation techniques including electroporation or other knownmethods. Activity of the Streptomyces azureus 23S rRNA A1067methyltransferase gene product can be used as a marker to select forRhodococcus opacus PD630 transformed with the transformation vector on,but not limited to, LB medium comprising thiostrepton. Growth mediasuitable Rhodococcus opacus PD630 lipid production include, but are notlimited to those culture media discussed by Kurosawa et al. and Alvarezet al. Evaluation of fatty acid profiles of Rhodococcus opacus PD630lipids can be assessed through standard lipid extraction and analyticalmethods described herein.

Example 34 Engineering Microalgae for Fatty Acid Auxotrophy

Strain B of Example 3, Prototheca moriformis (UTEX 1435) engineered toexpress a Cuphea wrightii thioesterase (CwTE2), was used as the hostorganism for further genetic modification to knockout both endogenousthioesterase alleles, FATA1-1 and FATA1-2. Here, a first transformationconstruct was generated to integrate a neomycin expression cassette intoStrain B at the FATA1-1 locus. This construct, pSZ2226, included 5′ (SEQID NO: 30) and 3′ (SEQ ID NO: 31) homologous recombination targetingsequences (flanking the construct) to the FATA1-1 locus of the nucleargenome and a neomycin resistance protein-coding sequence under thecontrol of the C. reinhardtii β-tubulin promoter/5′UTR (SEQ ID NO: 5)and the Chlorella vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). ThisNeoR expression cassette is listed as SEQ ID NO: 15 and served as aselectable marker.

Upon transformation of pSZ2226 into Strain B, individual transformantswere selected on agar plates comprising sucrose and G418. A singleisolate, Strain H, was selected for further genetic modification. Asecond transformation construct, pSZ2236, was generated to integratepolynucleotides enabling expression of a thiamine selectable marker intoStrain H at the FATA1-2 locus. pSZ2236 included 5′ (SEQ ID NO: 32) and3′ (SEQ ID NO: 33) homologous recombination targeting sequences(flanking the construct) to the FATA1-2 genomic region for integrationinto the P. moriformis (UTEX 1435) nuclear genome and an A. thalianaTHIC protein coding region under the control of the C. protothecoidesactin promoter/5′UTR (SEQ ID NO: 22) and C. vulgaris nitrate reductase3′ UTR (SEQ ID NO: 6). This AtTHIC expression cassette is listed as SEQID NO: 23 and served as a selectable marker. Upon transformation ofStrain H with pSZ2236 to generate Strain I, individual transformants,were selected on agar plates comprising free fatty acids. Strain I wasable to propagate on agar plates and in medium lacking thiamine andsupplemented with free fatty acids.

Example 35 Engineering Microorganisms for Increased Production ofStearic Acid

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain J, was transformed with the plasmid construct pSZ2281 accordingto biolistic transformation methods as described in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. pSZ2281 included polynucleotides encoding RNAhairpins (SAD2hpC, SEQ ID NO: 34) to down-regulate the expression ofstearoyl-ACP desaturase, 5′ (SEQ ID NO: 1) and 3′ (SEQ ID NO: 2)homologous recombination targeting sequences (flanking the construct) tothe 6S genomic region for integration into the nuclear genome, and a S.cerevisiae suc2 sucrose invertase coding region (SEQ ID NO: 4), toexpress the protein sequence given in SEQ ID NO: 3, under the control ofC. reinhardtii β-tubulin promoter/5′UTR (SEQ ID NO: 5) and Chlorellavulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). This S. cerevisiaesuc2 expression cassette is listed as SEQ ID NO: 7 and served as aselectable marker. The polynucleotide sequence encoding the SAD2hpC RNAhairpin was under the control of the C. protothecoides actinpromoter/5′UTR (SEQ ID NO: 22) and C. vulgaris nitrate reductase 3′ UTR(SEQ ID NO: 6).

Upon transformation of Strain J with construct pSZ2281, therebygenerating Strain K, positive clones were selected on agar platescontaining sucrose as a sole carbon source. Individual transformantswere clonally purified and propagated under heterotrophic conditionssuitable for lipid production as those detailed in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. Lipid samples were prepared from dried biomass andanalyzed using standard fatty acid methyl ester gas chromatography flameionization detection methods as described in Example 1 (also seePCT/US2012/023696). The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis UTEX Strain J propagated on glucoseas a sole carbon source and three representative isolates of Strain K,propagated on sucrose as a sole carbon source, are presented in Table21.

TABLE 21 Fatty acid profiles of Prototheca moriformis (UTEX 1435) cellsengineered to express a hairpin RNA construct targeting stearoyl ACPdesaturase gene/gene products. Area % Fatty acid Strain J Strain K-1Strain K-2 Strain K-3 Strain K-4 C8:0 0.02 C10:0 0.01 0.00 0.02 0.020.04 C12:0 0.03 0.05 0.05 0.05 0.08 C14:0 1.22 0.89 0.87 0.77 1.2 C16:026.75 29.23 28.96 27.55 28.06 C18:0 3.06 37.39 36.76 36.41 40.82 C18:159.62 23.90 24.76 26.92 22.02 C18:2 7.33 5.44 5.54 5.54 4.53 C18:3 0.14C20:0 1.43

The data presented in Table 21 show a clear impact of the expression ofSAD2 hairpin RNA construct on the C18:0 and C18:1 fatty acid profiles ofthe transformed organism. The fatty acid profiles of Strain Ktransformants comprising a SAD2 hairpin RNA construct demonstrated anincrease in the percentage of saturated C18:0 fatty acids with aconcomitant diminution of unsaturated C18:1 fatty acids. Fatty acidprofiles of the untransformed strain comprise about 3% C18:0. Fatty acidprofiles of the transformed strains comprise about 37% C18:0. These dataillustrate the successful expression and use of polynucleotides enablingexpression of a SAD RNA hairpin construct in Prototheca moriformis toalter the percentage of saturated fatty acids in the engineered hostmicrobes, and in particular in increasing the concentration of C18:0fatty acids and decreasing C18:1 fatty acids in microbial cells.

Also shown in Table 21, strain K-4 had a yet further elevated level ofstearate. Strain K4 was created by inserting the construct of strainsK1-K3 into the SAD2B locus. Thus, by knocking out one copy of the SADgene and inhibiting the remaining copies at the RNA level, a furtherreduction in oleic acid and corresponding increase in stearate wasobtained. Triglyceride analysis of RBD oil obtained from strain K4showed about 12% POP, 27% POS and 18% SOS.

Example 36 Engineering Microorganisms for Increased Production of OleicAcid Through Knockdown of an Endogenous Acyl-ACP Thioesterase

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain J, was transformed independently with each of the constructspSZ2402-pSZ2407 according to biolistic transformation methods asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Each of the constructspSZ2402-pSZ2407 included different polynucleotides encoding a hairpinRNA targeted against Prototheca moriformis FATA1 mRNA transcripts todown-regulate the expression of fatty acyl-ACP thioesterase, 5′ (SEQ IDNO: 1) and 3′ (SEQ ID NO: 2) homologous recombination targetingsequences (flanking the construct) to the 6S genomic region forintegration into the nuclear genome, and a S. cerevisiae suc2 sucroseinvertase coding region (SEQ ID NO: 4) to express the protein sequencegiven in SEQ ID NO: 3 under the control of C. reinhardtii β-tubulinpromoter/5′UTR (SEQ ID NO: 5) and Chlorella vulgaris nitrate reductase3′ UTR (SEQ ID NO: 6). This S. cerevisiae suc2 expression cassette islisted as SEQ ID NO: 7 and served as a selectable marker. Sequencelisting identities for the polynucleotides corresponding to each hairpinare listed in Table 22. The polynucleotide sequence encoding each RNAhairpin was under the control of the C. reinhardtii β-tubulinpromoter/5′UTR (SEQ ID NO: 5) and C. vulgaris nitrate reductase 3′ UTR(SEQ ID NO: 6).

TABLE 22 Plasmid constructs used to transform Prototheca moriformis(UTEX 1435) Strain J. Plasmid construct Hairpin designation SEQ ID NO:pSZ2402 PmFATA-hpB SEQ ID NO: 40 pSZ2403 PmFATA-hpC SEQ ID NO: 41pSZ2404 PmFATA-hpD SEQ ID NO: 42 pSZ2405 PmFATA-hpE SEQ ID NO: 43pSZ2406 PmFATA-hpF SEQ ID NO: 44 pSZ2407 PmFATA-hpG SEQ ID NO: 45

Upon independent transformation of Strain J with each of the constructslisted in Table 22, positive clones were selected on agar platescontaining sucrose as a sole carbon source. Individual transformantswere clonally purified and propagated under heterotrophic conditionssuitable for lipid production as those detailed in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. Lipid samples were prepared from dried biomass andanalyzed using standard fatty acid methyl ester gas chromatography flameionization detection methods as described in Example 1 (also seePCT/US2012/023696). The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis (UTEX 1435) Strain J propagated onglucose as a sole carbon source and representative isolates of eachtransformation of Strain J, propagated on sucrose as a sole carbonsource, are presented in Table 23.

TABLE 23 Fatty acid profiles of Prototheca moriformis (UTEX 1435) cellsengineered to express hairpin RNA constructs targeting fatty acyl-ACPthioesterase gene/gene products. Area % Fatty Acid Construct C10:0 C12:0C14:0 C16:0 C18:0 C18:1 C18:2 Strain J untransformed 0 0.05 1.32 26.663.1 59.07 7.39 PmFATA-hpB 0.04 0.07 1.36 24.88 2.24 61.92 6.84 0 0.081.33 25.34 2.39 61.72 6.5 0 0.07 1.29 25.44 2.26 61.7 6.69 0 0.06 1.3325.1 2.37 61.56 6.87 PmFATA-hpC 0 0.08 1.18 22.03 1.71 63.8 8.63 0 0.071.21 24.5 2.23 62.32 7.19 0 0.08 1.29 24.93 2.24 62.02 7.01 0.05 0.061.29 25.45 2.26 61.81 6.76 PmFATA-hpD 0 0.02 0.68 15.8 1.88 72.64 6.96 00.03 0.78 17.56 1.7 71.8 6.03 0 0.03 0.92 19.04 2.03 68.82 7.05 0 0.041.27 23.14 2.25 65.27 6.07 PmFATA-hpE 0 0.03 0.79 18.55 2.13 69.66 6.770 0.04 1.11 21.01 1.74 65.18 8.55 0 0.03 1.08 21.11 1.54 64.76 8.87 00.03 1.17 21.93 1.71 63.89 8.77 PmFATA-hpF 0.03 0.04 0.34 8.6 1.69 78.088.87 0 0.03 0.49 10.2 1.52 76.97 8.78 0 0.03 1 20.47 2.22 66.34 7.45 00.03 1.03 21.61 1.88 65.39 7.76 PmFATA-hpG 0 0.03 1.03 20.57 2.36 64.738.75 0 0.03 1.2 24.39 2.47 61.9 7.49 0 0.04 1.29 24.14 2.29 61.41 8.22

The data presented in Table 23 show a clear impact of the expression ofFATA hairpin RNA constructs on the C18:0 and C18:1 fatty acid profilesof the transformed organism. The fatty acid profiles of Strain Jtransformants comprising a FATA hairpin RNA construct demonstrated anincrease in the percentage of C18:1 fatty acids with a concomitantdiminution of C16:0 and C18:0 fatty acids. Fatty acid profiles of theuntransformed Strain J are about 26.66% C16:0, 3% C18:0, and about 59%C18:1 fatty acids. In contrast, the fatty acid profiles of thetransformed strains comprise as low as 8.6% C16:0 and 1.54% C18:0 andgreater than 78% C18:1 fatty acids.

These data illustrate the utility and successful use of polynucleotideFATA RNA hairpin constructs in Prototheca moriformis to alter the fattyacids profile of engineered microbes, and in particular in increasingthe concentration of C18:1 fatty acids and decreasing C18:0 and C16:0fatty acids in microbial cells.

Example 37 Engineering Microorganisms for Increased Production ofMid-Chain Fatty Acids Through KASI or KASIV Overexpression

This example describes the use of recombinant polynucleotides thatencode KASI or KASIV enzymes to engineer microorganisms in which thefatty acid profiles of the transformed microorganisms have been enrichedin lauric acid, C10:0, and total saturated fatty acids.

Each of the constructs pSZD1132, pSZD1133, pSZD1134, or pSZD1201 wasused independently to transform Strain B of Example 3, Protothecamoriformis (UTEX 1435) engineered to express a Cuphea wrightiithioesterase (CwTE2), according to biolistic transformation methods asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Each of the above constructsincluded different polynucleotides encoding a KASI or KASIV enzyme, 5′(SEQ ID NO: 13) and 3′ (SEQ ID NO: 14) homologous recombinationtargeting sequences (flanking the construct) to the pLoop genomic regionfor integration into the nuclear genome, and a neomycin resistanceprotein-coding sequence under the control of the C. reinhardtiiβ-tubulin promoter/5′UTR (SEQ ID NO: 5) and the Chlorella vulgarisnitrate reductase 3′ UTR (SEQ ID NO: 6). This NeoR expression cassetteis listed as SEQ ID NO: 15 and served as a selectable marker. Sequencelisting identities for the polynucleotides corresponding to eachconstruct are listed in Table 20. The polynucleotide sequence encodingeach KAS enzyme was under the control of the P. moriformis UTEX 1435Amt03 promoter/5′UTR (SEQ ID NO: 8) and C. vulgaris nitrate reductase 3′UTR (SEQ ID NO: 6). The protein coding regions of the KAS enzymes andneomycin resistance gene were codon optimized to reflect the codon biasinherent in P. moriformis UTEX 1435 nuclear genes as described inPCT/U52009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

Upon transformation of individual plasmids into Strain B, positiveclones were selected on agar plates comprising G418. Individualtransformants were clonally purified and grown on sucrose as a solecarbon source at pH 7.0 under conditions suitable for lipid productionas detailed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples were preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples were analyzed using standard fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1. The fatty acid profiles (expressed as Area % oftotal fatty acids) of Strain B and four positive transformants of eachof pSZ2046 (Strains M-P, 1-4) are presented in Table 24.

TABLE 24 Plasmid constructs used to transform Prototheca moriformis(UTEX 1435) Strain B. Plasmid KASI/KASIV Transit construct sourcepeptide SEQ ID NO: pSZD1134 Cuphea wrightii Native SEQ ID NO: 46 GenBankAccession No. U67317 pSZD1201 Cuphea wrightii PmSAD SEQ ID NO: 47pSZD1132 Cuphea pulcherrima Native SEQ ID NO: 48 GenBank Accession No.AAC68860 pSZD1133 Cuphea hookeriana Native SEQ ID NO: 49

TABLE 25 Fatty acid profiles of Prototheca moriformis (UTEX 1435) StrainB engineered for increased C10, lauric acid, and total saturated fattyacids. Fatty Acid (Area %) % Plasmid C10- Saturates/ construct(s) No.C10 C12 C14 C16 C18:0 C18:1 C18:2 C12 Total pSZ1283 7.89 35.49 16.5811.5 1.09 19.64 6.49 43.38 72.55 pSZ1283, 1 14.94 43.97 12.19 7.56 0.7214.11 5.31 58.91 79.38 pSZD1134 pSZ1283, 2 10.27 39.61 15.35 9.61 0.9417.1 5.88 49.88 75.78 pSZD1134 pSZ1283, 3 11.69 41.83 15.21 8.77 0.8315.04 5.40 53.52 78.33 pSZD1134 D1134-20 4 10.76 40.77 15.32 9.19 0.8816.06 5.76 51.53 76.92 pSZ1283, 1 10.77 40.31 15.21 9.43 0.88 16.18 5.9751.08 76.6 pSZD1132 pSZ1283, 2 9.19 37.03 15.02 10.52 1.00 19.63 6.2946.22 72.76 pSZD1132 pSZ1283, 3 8.97 36.09 15.01 10.77 1.05 20.38 6.3945.06 71.89 pSZD1132 pSZ1283, 4 9.51 38.12 14.96 9.96 0.94 18.93 6.3247.63 73.49 pSZD1132 pSZ1283, 1 13.06 46.21 9.84 7.12 0.75 16.7 5.2259.27 76.98 pSZD1201 pSZ1283, 2 11.02 43.91 13.01 7.78 0.86 16.53 5.7754.93 76.58 pSZD1201 pSZ1283, 3 11.59 45.14 12.41 7.61 0.82 15.72 5.6556.73 77.57 pSZD1201 pSZ1283, 4 10.66 41.32 13.74 8.75 0.68 18.64 5.2151.98 75.15 pSZD1201 pSZ1283, 1 6.90 36.08 15.15 11.02 1.00 21.74 6.7742.98 70.15 pSZD1133 pSZ1283, 2 7.01 35.88 15.01 10.75 1.07 22.02 6.9342.89 69.72 pSZD1133 pSZ1283, 3 10.65 41.94 12.38 8.48 0.85 18.28 6.1552.59 74.3 pSZD1133 pSZ1283, 4 10.23 41.88 12.58 8.52 0.82 18.48 6.2252.11 74.03 pSZD1133

The data presented in Table 25 show a clear impact of the exogenousexpression of KASI and KASIV enzymes on the C10:0 and C12 fatty acidprofiles of the transformed organism. The fatty acid profiles of StrainB, expressing the Cuphea wrightii thioesterase alone, comprised about 8%C10:0 and about 35.5% C12:0, with saturated fatty acids accounting for72.55% of total fatty acids. In contrast, transformants of Strain Bengineered to additionally express a Cuphea wrightii KASI with a P.moriformis stearoyl ACP desaturase transit peptide were characterized bya fatty acid profile of about 13% C10:0 and about 46% C12:0. Saturatedfatty acids accounted for as high as 77% in transformants of Strain Bco-expressing the C. wrightii KASI fusion protein. Similarly,transformants of Strain B engineered to express the C. wrightii KASIwith the enzyme's native transit peptide were characterized by a fattyacid profile of about 15% C10, about 44% C12, and about 79% saturatedfatty acids. The fatty acid profiles or many transformants of Strain Bexpressing either Cuphea pulcherrima KASIV or Cuphea hookeriana KASIValso displayed elevated C10% and C12% levels, compared to the fatty acidprofile of Strain B itself.

These data demonstrate the utility and effectiveness of polynucleotidesenabling expression of KASI and KASIV constructs in Protothecamoriformis (UTEX 1435) to alter the percentage of saturated fatty acidsin the engineered host microbes, and in particular in increasing theconcentration of C10:0 and C12:0 fatty acids in microbial cells.

Example 38 Engineering Microorganisms for Increased Production ofMid-Chain Fatty Acids Through KASI Knockout

This example describes the use of recombinant polynucleotides thatdisrupt different KASI alleles to engineer microorganisms in which thefatty acid profiles of the transformed microorganisms have been enrichedin C10:0 and midchain fatty acids.

Constructs pSZ2302 and pSZ2304 were used to independently transformStrain B of Example 3, Prototheca moriformis (UTEX 1435) engineered toexpress a Cuphea wrightii thioesterase (CwTE2), according to biolistictransformation methods as described in PCT/U52009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. pSZ2302 included 5′ (SEQ ID NO: 50) and 3′ (SEQ IDNO: 51) homologous recombination targeting sequences (flanking theconstruct) to the KAS1 allele 1 genomic region for integration into theP. moriformis nuclear genome, anA. thaliana THIC protein coding regionunder the control of the C. protothecoides actin promoter/5′UTR (SEQ IDNO: 22) and C. vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). pSZ2304included 5′ (SEQ ID NO: 52) and 3′ (SEQ ID NO: 53) homologousrecombination targeting sequences (flanking the construct) to the KAS1allele 2 genomic region for integration into the P. moriformis nucleargenome, anA. thaliana THIC protein coding region under the control ofthe C. protothecoides actin promoter/5′UTR (SEQ ID NO: 22) and C.vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6).This AtTHIC expressioncassette is listed as SEQ ID NO: 23 and served as a selection marker.The protein coding region of AtTHIC was codon optimized to reflect thecodon bias inherent in P. moriformis UTEX 1435 nuclear genes asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

Upon independent transformation pSZ2302 and pSZ2304 into Strain B,thereby generating Strain Q and R, positive clones were selected on agarplates comprising thiamine. Individual transformants were clonallypurified and cultivated on sucrose as a sole carbon source at pH 5.0 orpH 7.0 under heterotrophic conditions suitable for lipid production asdetailed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples were preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples were analyzed using fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1. The fatty acid profiles (expressed as Area % oftotal fatty acids) of Strain B and positive pSZ2302 (Strain Q, 1-5) andpSZ2304 (Strain R, 1-5) transformants are presented in Tables 26 and 27.

TABLE 26 Fatty acid profiles of Prototheca moriformis (UTEX 1435)Strains B, Q, and R engineered for increased midchain fatty acids,cultured at pH 5.0. Trans- Fatty Acid (Area %) formation C10- Strainplasmid(s) C10:0 C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 C14 UTEX 1435 None0.00 0.04 1.28 26.67 3.05 59.96 7.19 1.32 Strain B pSZ1283 0.01 0.091.09 21.60 2.21 65.15 7.94 1.19 Strain Q-1 pSZ1283, 0.08 1.21 7.52 38.711.38 38.32 8.75 8.81 pSZ2302 Strain Q-2 pSZ1283, 0.15 1.36 7.51 38.231.33 38.27 8.94 9.02 pSZ2302 Strain Q-3 pSZ1283, 0.16 1.43 7.49 38.881.30 37.58 8.73 9.08 pSZ2302 Strain Q-4 pSZ1283, 0.00 1.71 7.42 37.671.43 37.26 10.38 9.13 pSZ2302 Strain Q-5 pSZ1283, 0.13 1.21 7.36 38.811.31 38.07 8.71 8.7 pSZ2302 Strain R-1 pSZ1283, 0.19 1.78 8.47 40.111.34 33.46 9.98 10.44 pSZ2304 Strain R-2 pSZ1283, 0.90 8.00 7.78 28.961.15 30.26 17.14 16.68 pSZ2304 Strain R-3 pSZ1283, 0.26 3.58 7.77 34.981.56 32.86 14.60 11.61 pSZ2304 Strain R-4 pSZ1283, 1.64 13.50 7.61 21.380.90 36.13 14.73 22.75 pSZ2304 Strain R-5 pSZ1283, 1.03 9.63 7.56 25.611.00 31.70 18.23 18.22 pSZ2304

TABLE 27 Fatty acid profiles of Prototheca moriformis (UTEX 1435),Strains B, Q, and R engineered for increased midchain fatty acids,cultured at pH 7.0. Fatty Acid (Area %) Transformation C10- Strainplasmid(s) C10:0 C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 C14 UTEX None 0.010.04 1.34 27.94 3.24 57.46 7.88 1.39 1435 Strain B pSZ1283 4.72 29.5715.56 12.63 1.20 27.65 7.39 49.85 Strain Q-1 pSZ1283, pSZ2302 16.0050.61 9.52 5.33 0.54 11.79 5.28 76.13 Strain Q-2 pSZ1283, pSZ2302 16.3249.79 9.82 5.52 0.54 12.28 4.87 75.93 Strain Q-3 pSZ1283, pSZ2302 15.0847.58 10.23 5.93 0.56 15.12 4.50 72.89 Strain Q-4 pSZ1283, pSZ2302 14.2747.30 10.44 6.17 0.56 15.50 4.59 72.01 Strain Q-5 pSZ1283, pSZ2302 14.7547.28 10.32 6.04 0.59 15.50 4.65 72.35 Strain R-1 pSZ1283, pSZ2304 21.2555.42 7.97 3.65 0.00 5.46 5.66 84.64 Strain R-2 pSZ1283, pSZ2304 13.0055.05 10.88 5.78 0.28 7.90 6.29 78.93 Strain R-3 pSZ1283, pSZ2304 12.8953.15 11.11 6.13 0.00 9.87 6.13 77.15 Strain R-4 pSZ1283, pSZ2304 12.8051.64 13.86 6.69 0.00 7.51 6.70 78.3 Strain R-5 pSZ1283, pSZ2304 16.6151.42 9.84 5.27 0.33 11.15 4.79 77.87

The data presented in Tables 26 and 27 show a clear impact of disruptionof different KASI alleles on the fatty acid profiles of the transformedorganisms. When cultivated at pH 5.0, the fatty acid profiles ofPrototheca moriformis (UTEX 1435) and Prototheca moriformis (UTEX 1435)Strain B, expressing a Cuphea wrightii FATB2 thioesterase under controlof a pH regulatable promoter were very similar. These profiles werecharacterized by about 1% C14:0, about 21-26% C16:0, about 2-3% C18:0,about 60-65% C18:1, about 7% C18:2, with C10-C14 fatty acids comprisingabout 1.19-1.3% of total fatty acids. In contrast, when cultivated at pH5.0, Strain B further engineered to disrupt KASI allele 1 (Strain Q) orKASI allele 2 (Strain R) demonstrated altered fatty acid profiles thatwere characterized by increased levels of C12, increased levels of C14,decreased levels of C18, and decreased levels of C18:1 fatty acidscompared to Strain B or UTEX 1435. The fatty acid profiles of isolatesof Strains Q and R differed in that Strain R (allele 2 knockout)isolates had generally greater C12s and lower C16s and C18:1s thanStrain Q (allele 1 knockout).

When cultivated at pH 7.0, the fatty acid profile of Protothecamoriformis (UTEX 1435) is distinct from that Prototheca moriformis (UTEX1435) Strain B expressing a Cuphea wrightii FATB2 thioesterase undercontrol of a pH regulatable promoter. When cultured at pH 7.0, Strain Bwas characterized by a fatty acid profile elevated in C10, C12, and C14fatty acids (these comprised about 50% of the total fatty acids). Whencultured at pH 7.0, Strain Q and Strain R demonstrated fatty acidprofiles with still further increases in C10, C12, and C14 fatty acidsand still further decreases in C18:0 and C18:1 fatty acids relative tothat of Strain B. Again, differences in fatty acid profiles betweenStrain Q and R were observed with the profile of Strain R comprisinggreater percentage levels of C12 and lower levels of C18:1 than that ofStrain Q.

These data illustrate the successful expression and use ofpolynucleotides enabling expression of KASI and KASIV constructs inPrototheca moriformis to alter the percentage of saturated fatty acidsin the engineered host microbes, and in particular in increasing theconcentration of C10:0 and C12:0 fatty acids and decreasing theconcentration of C18:0 and C18:1 fatty acids in microbial cells. Inaddition, the data here indicate the different KASI alleles can bedisrupted to result in altered fatty acid profiles of the transformedorganisms.

Example 39 Engineering Microorganisms for Increased Production ofMid-Chain Fatty Acids Through KASI Knockdown

This example describes the use of recombinant polynucleotides thatencode RNA hairpins to attenuate a KASI enzyme to engineer amicroorganism in which the fatty acid profile of the transformedmicroorganism has been enriched in midchain fatty acids.

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain S, was transformed independently with each of the constructspSZ2482-pSZ2485 according to biolistic transformation methods asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Each of the constructspSZ2482-pSZ2485 included different polynucleotides encoding hairpin RNAstargeted against Prototheca moriformis (UTEX 1435) KASI mRNA transcriptsto down-regulate the expression of fatty acyl-ACP thioesterase, 5′ (SEQID NO: 1) and 3′ (SEQ ID NO: 2) homologous recombination targetingsequences (flanking the construct) to the 6S genomic region forintegration into the nuclear genome, and a S. cerevisiae suc2 sucroseinvertase coding region (SEQ ID NO: 4) to express the protein sequencegiven in SEQ ID NO: 3 under the control of C. reinhardtii β-tubulinpromoter/5′UTR (SEQ ID NO: 5) and Chlorella vulgaris nitrate reductase3′ UTR (SEQ ID NO: 6). This S. cerevisiae suc2 expression cassette islisted as SEQ ID NO: 7 and served as a selectable marker. Sequencelisting identities for the polynucleotides corresponding to each KASIhairpin are listed in Table 28. The polynucleotide sequence encodingeach RNA hairpin was under the control of the P. moriformis Amt03promoter/5′UTR (SEQ ID NO: 8) and C. vulgaris nitrate reductase 3′ UTR(SEQ ID NO: 6). The protein coding region of the suc2 expressioncassette was codon optimized to reflect the codon bias inherent in P.moriformis UTEX 1435 nuclear genes as described in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696.

TABLE 28 Plasmid constructs used to transform Prototheca moriformis(UTEX 1435) Strain S. Transformation construct Hairpin SEQ ID NO:pSZ2482 KASI hairpin B SEQ ID NO: 54 pSZ2483 KASI hairpin C SEQ ID NO:55 pSZ2484 KASI hairpin D SEQ ID NO: 56 pSZ2485 KASI hairpin E SEQ IDNO: 57

Upon independent transformation of Strain S with each of the constructslisted in Table 28, positive clones were selected on agar platescontaining sucrose as a sole carbon source. Individual transformantswere clonally purified and propagated under heterotrophic conditionssuitable for lipid production as those detailed in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. Lipid samples were prepared from dried biomass andanalyzed using fatty acid methyl ester gas chromatography flameionization detection methods as described in Example 1 (also seePCT/US2012/023696). The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis UTEX 1435 propagated on glucose as asole carbon source and four representative isolates of eachtransformation of Strain S, propagated on sucrose as a sole carbonsource, are presented in Table 29.

TABLE 29 Fatty acid profiles of Prototheca moriformis (UTEX 1435) cellsengineered to express hairpin RNA constructs targeting KASI gene/geneproducts. Fatty Acid (Area %) Strain Plasmid Number C10:0 C12:0 C14:0C16:0 C18:0 C18:1 C18:2 C18:3 UTEX 1435 none 1 0.00 0.04 1.45 27.97 3.1858.35 6.78 0.60 Strain S pSZ2482 1 0.19 0.74 8.47 38.30 2.15 36.24 9.451.42 2 0.07 0.25 4.16 32.46 2.62 49.57 7.73 0.82 3 0.03 0.10 2.68 27.482.65 56.40 8.14 0.55 4 0.03 0.10 2.60 27.44 2.01 55.54 9.15 0.78 pSZ24831 0.00 0.06 1.94 30.58 1.55 53.26 9.31 0.76 2 0.20 0.05 1.76 28.01 2.3156.61 8.70 0.60 3 0.00 0.06 1.60 24.38 2.65 58.25 9.93 1.15 4 0.00 0.041.56 26.65 2.96 60.06 6.92 0.52 pSZ2484 1 0.72 3.71 19.15 38.03 1.6814.22 15.00 4.21 2 0.66 2.76 16.34 38.19 1.78 18.52 14.91 3.38 3 0.692.96 16.20 37.28 1.77 19.05 15.26 3.48 4 0.18 0.70 8.61 36.80 2.35 36.2210.89 1.10 pSZ2485 1 0.00 0.04 1.41 25.34 3.16 60.12 7.78 0.48 2 0.030.04 1.41 23.85 2.19 61.23 8.75 0.67 3 0.00 0.04 1.41 24.41 2.23 60.648.69 0.67 4 0.00 0.04 1.41 24.51 2.16 60.85 8.91 0.66

The data presented in Table 29 show a clear impact of the expression ofKAS hairpin RNA constructs on the fatty acid profiles of the transformedorganisms. The fatty acid profiles of Strain S transformants comprisingeither pSZ2482 or pSZ2484 KASI hairpin RNA construct demonstrated anincrease in the percentage of C10, C12, C14, and C16 fatty acids with aconcomitant diminution of C18:0 and C18:1 fatty acids relative to thefatty acid profile of UTEX 1435.

These data illustrate the utility and successful use of polynucleotideKASI RNA hairpin constructs in Prototheca moriformis (UTEX 1435) toalter the fatty acids profile of engineered microbes, and in particularin increasing the concentration of midchain fatty acids and decreasingC18:0 and C18:1 fatty acids in microbial cells.

Example 40 Engineering Microorganisms for Increased Production ofStearic Acid Through Fatty Acid Elongase Overexpression

This example describes the use of recombinant polynucleotides thatencode fatty acid elongases to engineer a microorganism in which thefatty acid profile of the transformed microorganism has been enriched instearic acid, arachidic acid, and docosadienoic acid.

A classically mutagenized strain of Prototheca moriformis (UTEX 1435),Strain J, was transformed independently with each of the constructspSZ2323, pSZ2324, or pSZ2328 according to biolistic transformationmethods as described in PCT/US2009/066141, PCT/US2009/066142,PCT/US2011/038463, PCT/US2011/038464, and PCT/US2012/023696. Each of theconstructs included a protein coding region to overexpress an elongase,5′ (SEQ ID NO: 1) and 3′ (SEQ ID NO: 2) homologous recombinationtargeting sequences (flanking the construct) to the 6S genomic regionfor integration into the nuclear genome, and a S. cerevisiae suc2sucrose invertase coding region (SEQ ID NO: 4) to express the proteinsequence given in SEQ ID NO: 3 under the control of C. reinhardtiiβ-tubulin promoter/5′UTR (SEQ ID NO: 5) and Chlorella vulgaris nitratereductase 3′ UTR (SEQ ID NO: 6). This S. cerevisiae suc2 expressioncassette is listed as SEQ ID NO: 7 and served as a selectable marker.Sequence listing identities for the polynucleotides corresponding toeach elongase are listed in Table 30. The polynucleotide sequenceencoding each elongase was under control of the P. moriformis Amt03promoter/5′UTR (SEQ ID NO: 8) and C. vulgaris nitrate reductase 3′ UTR(SEQ ID NO: 6). The protein coding regions of the exogenous elongasesand the suc2 expression cassette were codon optimized to reflect thecodon bias inherent in P. moriformis UTEX 1435 nuclear genes asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

TABLE 30 Plasmid constructs used to transform Prototheca moriformis(UTEX 1435) Strain J. Plasmid GenBank construct Elongase sourceAccession No. SEQ ID NO: pSZ2328 Marchantia polymorpha AAP74370 58, 59pSZ2324 Trypanosoma brucei AAX70673 60, 61 pSZ2323 Saccharomycescerevisiae P39540 62, 63

Upon independent transformation of Strain J with the constructs listedin Table 30, positive clones were selected on agar plates containingsucrose as a sole carbon source. Individual transformants were clonallypurified and propagated under heterotrophic conditions suitable forlipid production as those detailed in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. Lipid samples were prepared from dried biomass andanalyzed using fatty acid methyl ester gas chromatography flameionization detection methods as described in Example 1 (also seePCT/US2012/023696). The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis UTEX 1435 Strain J propagated onglucose as a sole carbon source and three representative isolates ofeach transformation of Strain J, propagated on sucrose as a sole carbonsource are presented in Table 31.

TABLE 31 Fatty acid profiles of Prototheca moriformis (UTEX 1435) StrainJ cells engineered to overexpress elongases. Fatty Acid Area % PlasmidC14: C16: C16: C18: C18: C18: C18: C20: C22: construct No. 0 0 1 0 1 23α 0 2n6 None 1 1.39 27.42 0.77 3.33 57.46  8.05 0.61 0.30 0.03 pSZ23281 1.25 19.23 0.85 8.26 57.54  9.34 0.79 0.73 0.94 pSZ2328 2 1.22 17.760.69 7.86 60.56  9.38 0.59 0.6  0.47 pSZ2328 3 1.26 18.37 0.92 7.8358.77 10.01 0.72 0.64 0.52 pSZ2324 1 1.51 22.97 1.09 8.71 53.01  9.630.65 0.68 0.55 pSZ2324 2 1.29 20.6  0.92 7.53 56.97  9.92 0.73 0.64 0.43pSZ2324 3 1.28 20.59 0.93 7.33 57.52  9.68 0.65 0.58 0.42 pSZ2323 1 1.6527.27 0.67 3.56 56.68  8.72 0.33 0.36 0.00 pSZ2323 2 1.56 28.44 0.743.36 55.22  9.07 0.46 0.39 0.03 pSZ2323 3 1.64 28.7  0.75 3.34 55.29 8.59 0.49 0.36 0.02

The data presented in Table 31 show a clear impact of the expression ofMarchantia polymorpha and Trypanosoma brucei enzymes on the C14, C16,C18:0, C20:0, and C22:2n6 fatty acid profiles of the transformedorganisms. The fatty acid profile of untransformed Strain J was about27.42% C16:0, about 3% C18:0, about 57.5% C18:1, about 0.3% C20:0 andabout 0.03% C22:2n6 fatty acids. In contrast to that of Strain J, thefatty acid profiles of Strain J transformed with different plasmidconstructs to express elongases comprised lower percentage levels of C16and higher percentage levels of C18:0, C20:0, and C22:2n6 fatty acids.The result of overexpression of Marchantia polymorpha elongase was abouta 2.5 fold increase in percentage levels of C18:0 fatty acids, a 2 foldincrease in percentage levels of C20:0 fatty acids, and about a 15 to 30fold increase in percentage levels of C22:2n6 fatty acids relative tothe fatty acid profile of Strain J.

These data illustrate the successful use of polynucleotides encodingelongases for expression in Prototheca moriformis (UTEX 1435) to alterthe fatty acid profile of engineered microbes, and in particular inincreasing the concentration of C18:0, C20:0, and C22:2n6 fatty acidsand decreasing C16:0 fatty acids in recombinant microbial cells.

Example 41 Engineering Microorganisms for Increased Production ofStearic Acid Through Acyl-ACP Thioesterase Overexpression

This example describes the use of recombinant polynucleotides thatencode different C18:0-preferring acyl-ACP thioesterases to engineermicroorganisms in which the fatty acid profiles of the transformedmicroorganisms have been enriched in stearic acid.

Classically mutagenized strains of Prototheca moriformis (UTEX 1435),Strain J or Strain A, were transformed independently with the constructslisted in Table 32 according to biolistic transformation methods asdescribed in PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Each of the constructsincluded a protein coding region to overexpress a fatty acyl-ACPthioesterase with a C-terminal 3× FLAG® epitope tag, 5′ (SEQ ID NO: 1)and 3′ (SEQ ID NO: 2) homologous recombination targeting sequences(flanking the construct) to the 6S genomic region for integration intothe nuclear genome, and a S. cerevisiae suc2 sucrose invertase codingregion (SEQ ID NO: 4) to express the protein sequence given in SEQ IDNO: 3 under the control of C. reinhardtii β-tubulin promoter/5′UTR (SEQID NO: 5) and Chlorella vulgaris nitrate reductase 3′ UTR (SEQ ID NO:6). This S. cerevisiae suc2 expression cassette is listed as SEQ ID NO:7 and served as a selectable marker. Sequence listing identities for thepolynucleotides corresponding to each thioesterase are listed in Table32. The polynucleotide sequence encoding each thioesterase was undercontrol of the P. moriformis Amt03 promoter/5′UTR (SEQ ID NO: 8) and C.vulgaris nitrate reductase 3′ UTR (SEQ ID NO: 6). The protein codingregions of the exogenous thioesterases and the suc2 expression cassettewere codon optimized to reflect the codon bias inherent in P. moriformisUTEX 1435 nuclear genes as described in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696.

TABLE 32 Plasmid constructs used to transform Prototheca moriformis(UTEX 1435) Strain A or Strain J. Acyl-ACP Thioesterase, Acyl-ACPTransit Plasmid GenBank Thioesterase Peptide construct Accession No.source source SEQ ID NO: pSZD581 FATA, Brassica napus native 64, 65CAA52070 pSZD643 FATA, Brassica napus UTEX 66, 67 CAA52070 250 SADpSZD645 FATA, C. tinctorius UTEX 68, 69 AAA33019 250 SAD pSZD644 FATA,Ricinis communis native 70, 71 ABS30422 pSZD1323 FATA, G. mangostananative 72, 73 AAB51523 pSZD1320 FATA Theobroma cacao native 74, 75

Upon independent transformation of Strain A or J with the constructslisted in Table 32, positive clones were selected on agar platescontaining sucrose as a sole carbon source. Individual transformantswere clonally purified and propagated under heterotrophic conditionssuitable for lipid production as those detailed in PCT/US2009/066141,PCT/US2009/066142, PCT/US2011/038463, PCT/US2011/038464, andPCT/US2012/023696. Lipid samples were prepared from dried biomass andanalyzed using fatty acid methyl ester gas chromatography flameionization detection methods as described in Example 1 (also seePCT/US2012/023696). The fatty acid profiles (expressed as Area % oftotal fatty acids) of P. moriformis UTEX 1435 Strain J propagated onglucose as a sole carbon source and representative isolates of eachtransformation of Strain J, propagated on sucrose as a sole carbonsource are presented in Table 33.

TABLE 33 Fatty acid profiles of Prototheca moriformis (UTEX 1435) StrainJ cells engineered to overexpress exogenous acyl-ACP thioesteraseenzymes. Plasmid Fatty Acid Area % Strain construct No. C14:0 C16:0C18:0 C18:1 C18:2 C18:3α A None 1 1.08 25.48 3.23 59.70 8.25 0.70 J None1 1.41 27.33 3.38 57.07 8.15 0.64 A pSZD581 1 1.02 26.60 14.47 44.8010.05 0.65 2 1.08 28.24 13.57 43.89 10.07 0.68 3 0.97 24.70 9.13 50.8511.27 0.82 A pSZD643 1 1.39 26.97 16.21 44.10 8.43 0.83 2 1.37 27.9111.15 48.31 8.40 0.78 A pSZD645 1 0.90 23.39 8.35 50.69 13.34 0.96 ApSZD644 1 1.67 19.70 4.40 59.15 12.32 1.01 J pSZD1323 1 1.33 23.26 9.2853.42 10.35 0.69 2 1.47 26.84 7.36 52.78 9.29 0.64 3 1.43 26.31 6.0554.45 9.37 0.66 J pSZD1320 1 1.30 24.76 3.84 60.90 6.96 0.55 2 1.3626.30 3.27 58.19 8.66 0.48 3 1.39 25.51 3.18 58.78 8.85 0.45

The data presented in Table 33 show a clear impact of the expression ofexogenous acyl-ACP enzymes on the fatty acid profiles of the transformedmicroorganisms. The fatty acid profiles of untransformed Strain A and Jwere about 25% C16:0, about 3.3% C18:0, about 57 to 60% C18:1. Incontrast, the fatty acid profiles of Strain A transformed with differentplasmid constructs to express acyl-ACP enzymes comprised greaterpercentage levels of C18:0 and lower percentage levels of C18:1 fattyacids than that of Strain A. Expression of FATA enzymes from B. napus,C. tinctorius, R. communis and G. mangostana in Strain A or J enabledthe accumulation of stearate levels in the transformed organisms. Theresult of overexpression of a Brassica napus acyl-ACP thioesterase wasabout a 2 to 5 fold increase in the percentage levels of C18:0 fattyacids of the fatty acid profile of the transformed organisms relative tothe fatty acid profile of Strain A. Fatty acid profiles of cellsengineered to overexpress a G. mangostana acyl-ACP FATA thioesterasewith a C. protothecoides SAD1 transit peptide were characterized byabout a 2 to 3 fold increase in the percentage levels of C18:0 fattyacids of the fatty acid profile of the transformed organism relative tothe fatty acid profile of Strain J.

These data illustrate the utility and effective use of polynucleotidesencoding fatty acyl-ACP thioesterases for expression in Protothecamoriformis (UTEX 1435) to alter the fatty acid profile of engineeredmicrobes, and in particular in increasing the concentration of C18:0 anddecreasing C18:1 fatty acids in recombinant microbial cells.

Example 42 Engineering Microorganisms for Increased Production of ErucicAcid Through Elongase or Beta-Ketoacyl-COA Synthase Overexpression

In an embodiment of the present invention, a recombinant polynucleotidetransformation vector operable to express an exogenous elongase orbeta-ketoacyl-CoA synthase in an optionally plastidic oleaginous microbeis constructed and employed to transform Prototheca moriformis (UTEX1435) according to the biolistic transformation methods as described inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696 to obtain a cell increased forproduction of erucic acid. The transformation vector includes a proteincoding region to overexpress an elongase or beta-ketoacyl-CoA synthasesuch as those listed in Table 5, promoter and 3′UTR control sequences toregulate expression of the exogenous gene, 5′ and 3′ homologousrecombination targeting sequences targeting the recombinantpolynucleotides for integration into the P. moriformis (UTEX 1435)nuclear genome, and nucleotides operable to express a selectable marker.The protein-coding sequences of the transformation vector arecodon-optimized for expression in P. moriformis (UTEX 1435) as describedin PCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Recombinant polynucleotidesencoding promoters, 3′ UTRs, and selectable markers operable forexpression in P. moriformis (UTEX 1435) are disclosed herein and inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696.

Upon transformation of the transformation vector into P. moriformis(UTEX 1435) or a classically-mutagenized strain of P. moriformis (UTEX1435), positive clones are selected on agar plates. Individualtransformants are clonally purified and cultivated under heterotrophicconditions suitable for lipid production as detailed inPCT/US2009/066141, PCT/US2009/066142, PCT/US2011/038463,PCT/US2011/038464, and PCT/US2012/023696. Lipid samples are preparedfrom dried biomass from each transformant and fatty acid profiles fromthese samples are analyzed using fatty acid methyl ester gaschromatography flame ionization (FAME GC/FID) detection methods asdescribed in Example 1. As a result of these manipulations, the cell mayexhibit an increase in erucic acid of at least 5, 10, 15, or 20 fold.

Example 43 Generation Of Capric, Lauric, and Myristic Acid Rich Oils inStrain UTEX1435 by the Expression of Cuphea PSR23 LPAATs

We tested the effect of expression of two 1-acyl-sn-glycerol-3-phosphateacyltransferases (LPAATs) in a previously described P. moriformis (UTEX1435) transgenic strain, expressing the acyl ACP thioesterase (FATB2)from Cuphea wrightii. The LPAAT2 and LPAAT3 genes from Cuphea PSR23(CuPSR23) were identified by analysis of a combination of CuPSR23genomic sequences and transcriptomic sequences derived from seed RNAs.The two LPAATs have not been previously described. The genes were codonoptimized to reflect UTEX 1435 codon usage. Transformations, cellculture, lipid production and fatty acid analysis were all carried outas previously described.

Increased capric, lauric, and myristic accumulation in strain B by theexpression of the Cuphea PSR23 1-acyl-sn-glycerol-3-phosphateacyltransferases (LPAAT2 and LPAAT3) [pSZ2299 and pSZ2300,respectively]: In this example, transgenic strains were generated viatransformation of strain B with the constructs pSZ2299 or pSZ2300,encoding CuPSR23 LPAAT2 and LPAAT3, respectively. The transgenic strainswere selected for resistance to the antibiotic G418. Construct pSZ2299can be written aspLOOP5′::CrTUB2:NeoR:CvNR::PmAMT3:CuPSR23LPAAT2-1:CvNR::pLOOP3′.Construct pSZ2300 can be written aspLOOP5′::CrTUB2:NeoR:CvNR::PmAMT3:CuPSR23LPAAT3-1:CvNR::pLOOP3′. Thesequence of the transforming DNA (pSZ2299 and pSZ2300) is providedbelow. The relevant restriction sites in the construct from 5′-3′,BspQI, KpnI, XbaI, Mfe I, BamHI, EcoRI, SpeI, XhoI, SacI, BspQI,respectively, are indicated in lowercase, bold, and underlined. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences at the 5′ and 3′ end of the construct representgenomic DNA from UTEX 1435 that target integration to the pLoop locusvia homologous recombination. Proceeding in the 5′ to 3′ direction, theselection cassette has the C. reinhardtii β-tubulin promoter drivingexpression of the NeoR gene (conferring resistance to G418) and theChlorella vulgaris Nitrate Reductase (NR) gene 3′ UTR. The promoter isindicated by lowercase, boxed text. The initiator ATG and terminator TGAfor NeoR are indicated by uppercase italics, while the coding region isindicated with lowercase italics. The 3′ UTR is indicated by lowercaseunderlined text. The spacer region between the two cassettes isindicated by upper case text. The second cassette containing the codonoptimized LPAAT2 gene (pSZ2299) or LPAAT3 gene (pSZ2300) from CupheaPSR23 is driven by the Prototheca moriformis endogenous AMT3 promoter,and has the same Chlorella vulgaris Nitrate Reductase (NR) gene 3′ UTR.In this cassette, the AMT3 promoter in indicated by lowercase, boxedtext. The initiator ATG and terminator TGA for the CuPSR23 LPAAT2 andLPAAT3 genes are indicated in uppercase italics, while the codingregions are indicated by lowercase italics. The 3′ UTR is indicated bylowercase underlined text. The final constructs were sequenced to ensurecorrect reading frames and targeting sequences.

pSZ2299 Transforming Construct: (SEQ ID NO:90) gctcttccgctaacggaggtctgtcaccaaatggaccccgtctattgcgggaaaccacggcgatggcacgtttcaaaacttgatgaaatacaatattcagtatgtcgcgggcggcgacggcggggagctgatgtcgcgctgggtattgcttaatcgccagcttcgcccccgtcttggcgcgaggcgtgaacaagccgaccgatgtgcacgagcaaatcctgacactagaagggctgactcgcccggcacggctgaattacacaggcttgcaaaaataccagaatttgcacgcaccgtattcgcggtattttgttggacagtgaatagcgatgcggcaatggcttgtggcgttagaaggtgcgacgaaggtggtgccaccactgtgccagccagtcctggcggctcccagggccccgatcaagagccaggacatccaaactacccacagcatcaacgccccggcctatactcgaaccccacttgcactctgcaatggtatgggaa

ccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatccCGCGTCTCGAACAGAGCGCGCAGAGGAACGCTGAAGGTCTCGCCTCTGTCGCACCTCAGCGCGGCATACACCACAATAACCACCTGACGAATGCGCTTGGTTCTTCGTCCATTAGCGAAGCGTCCGGTTCACACACGTGCCACGTTGGCGAGGTGGCAGGTGACAATGATCG

cctgatcatcaacctgttccaggcgctgtgcttcgtcctgatccgccccctgtccaagaacgcctaccgccgcatcaaccgcgtgttcgcggagctgctgctgtccgagctgctgtgcctgttcgactggtgggcgggcgcgaagctgaagctgttcaccgaccccgagacgttccgcctgatgggcaaggagcacgccctggtcatcatcaaccacatgaccgagctggactggatggtgggctgggtgatgggccagcacttcggctgcctgggctccatcatctccgtcgccaagaagtccacgaagttcctgcccgtgctgggctggtccatgtggttctccgagtacctgtacctggagcgctcctgggccaaggacaagtccaccctgaagtcccacatcgagcgcctgatcgactaccccctgcccttctggctggtcatcttcgtcgagggcacccgcttcacgcgcacgaagctgctggcggcccagcagtacgcggtctcctccggcctgcccgtcccccgcaacgtcctgatcccccgcacgaagggcttcgtctcctgcgtgtcccacatgcgctccttcgtccccgcggtgtacgacgtcacggtggcgttccccaagacgtcccccccccccacgctgctgaacctgttcgagggccagtccatcatgctgcacgtgcacatcaagcgccacgccatgaaggacctgcccgagtccgacgacgccgtcgcggagtggtgccgcgacaagttcgtcgagaaggacgccctgctggacaagcacaacgcggaggacacgttctccggccaggaggtgtgccactccggctcccgccagctgaagtccctgctggtcgtgatctcctgggtcgtggtgacgacgttcggcgccctgaagttcctgcagtggtcctcctggaagggcaaggcgttctccgccatcggcctgggcatcgtcaccctgctgatgcacgtgctgatcctgtcctcccaggccgagcgctccaaccccgccgaggtggcccaggccaagctgaagaccggcctgtccatctccaagaaggtgacggacaaggagaacTGAttaattaactcgaggcagcagcaptcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctt gagctcagcggcgacggtcctgctaccgtacgacgttgggcacgcccatgaaagtttgtataccgagcttgttgagcgaactgcaagcgcggctcaaggatacttgaactcctggattgatatcggtccaataatggatggaaaatccgaacctcgtgcaagaactgagcaaacctcgttacatggatgcacagtcgccagtccaatgaacattgaagtgagcgaactgttcgcttcggtggcagtactactcaaagaatgagctgctgttaaaaatgcactctcgttctctcaagtgagtggcagatgagtgctcacgccttgcacttcgctgcccgtgtcatgccctgcgccccaaaatttgaaaaaagggatgagattattgggcaatggacgacgtcgtcgctccgggagtcaggaccggcggaaaataagaggcaacacactccgcttctta gctcttcg  pSZ2300 Transforming Construct: (SEQ ID NO:91) gctcttccgctaacggaggtctgtcaccaaatggaccccgtctattgcgggaaaccacggcgatggcacgtttcaaaacttgatgaaatacaatattcagtatgtcgcgggcggcgacggcggggagctgatgtcgcgctgggtattgcttaatcgccagcttcgcccccgtcttggcgcgaggcgtgaacaagccgaccgatgtgcacgagcaaatcctgacactagaagggctgactcgcccggcacggctgaattacacaggcttgcaaaaataccagaatttgcacgcaccgtattcgcggtattttgttggacagtgaatagcgatgcggcaatggcttgtggcgttagaaggtgcgacgaaggtggtgccaccactgtgccagccagtcctggcggctcccagggccccgatcaagagccaggacatccaaactacccacagcatcaacgccccggcctatactcgaaccccacttgcactctgcaatggtatgggaa

gccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatccCGCGTCTCGAACAGAGCGCGCAGAGGAACGCTGAAGGTCTCGCCTCTGTCGCACCTCAGCGCGGCATACACCACAATAACCACCTGACGAATGCGCTTGGTTCTTCGTCCATTAGCGAAGCGTCCGGTTCACACACGTGCCACGTTGGCGAGGTGGCAGGTGACAATGATC

tgatcgtcaacctggtgcaggccgtctgcttcgtcctgatccgccccctgtccaagaacacgtaccgccgcatcaaccgcgtggtcgcggagctgctgtggctggagctggtgtggctgatcgactggtgggcgggcgtgaagatcaaggtcttcacggaccacgagacgttccacctgatgggcaaggagcacgccctggtcatctgcaaccacaagtccgacatcgactggctggtcggctgggtcctgggccagcgctccggctgcctgggctccaccctggcggtcatgaagaagtcctccaagttcctgcccgtcctgggctggtccatgtggttctccgagtacctgttcctggagcgctcctgggccaaggacgagatcacgctgaagtccggcctgaaccgcctgaaggactaccccctgcccttctggctggcgctgttcgtggagggcacgcgcttcacccgcgcgaagctgctggcggcgcagcagtacgccgcgtcctccggcctgcccgtgccccgcaacgtgctgatcccccgcacgaagggcttcgtgtcctccgtgtcccacatgcgctccttcgtgcccgcgatctacgacgtcaccgtggccatccccaagacgtcccccccccccacgctgatccgcatgttcaagggccagtcctccgtgctgcacgtgcacctgaagcgccacctgatgaaggacctgcccgagtccgacgacgccgtcgcgcagtggtgccgcgacatcttcgtggagaaggacgcgctgctggacaagcacaacgccgaggacaccttctccggccaggagctgcaggagaccggccgccccatcaagtccctgctggtcgtcatctcctgggccgtcctggaggtgttcggcgccgtcaagttcctgcagtggtcctccctgctgtcctcctggaagggcctggcgttctccggcatcggcctgggcgtgatcaccctgctgatgcacatcctgatcctgttctcccagtccgagcgctccacccccgccaaggtggcccccgcgaagcccaagaacgagggcgagtcctccaagaccgagatggagaaggagaagTGAttaattaactcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatcccatccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctt gagctcagcggcgacggtcctgctaccgtacgacgttgggcacgcccatgaaagtttgtataccgagcttgttgagcgaactgcaagcgcggctcaaggatacttgaactcctggattgatatcggtccaataatggatggaaaatccgaacctcgtgcaagaactgagcaaacctcgttacatggatgcacagtcgccagtccaatgaacattgaagtgagcgaactgttcgcttcggtggcagtactactcaaagaatgagctgctgttaaaaatgcactctcgttctctcaagtgagtggcagatgagtgctcacgcctgcacttcgctgcccgtgtcatgccctgcgccccaaaatttgaaaaaagggatgagattattgggcaatggacgacgtcgtcgctccgggagtcaggaccggcggaaaataagaggcaacacactccgcttctta gctcttcg

To determine the impact of the CuPSR23 LPAAT2 and LPAAT3 genes onmid-chain fatty acid accumulation, the above constructs containing thecodon optimized CuPSR23 LPAAT2 or LPAAT3 genes driven by the UTEX 1453AMT3 promoter were transformed into strain B.

Primary transformants were clonally purified and grown under standardlipid production conditions at pH7.0 (all the strains require growth atpH 7.0 to allow for maximal expression of the CuPSR23 LPAAT2 or LPAAT3gene driven by the pH-regulated AMT3 promoter). The resulting profilesfrom a set of representative clones arising from these transformationsare shown in Table 34, below. D1520 represents clones of Strain B withCuPSR23 LPAAT2 and D1521 represents clones of Strain B with CuPSR23LPAAT3.

TABLE 34 Fatty acid profiles of Strain B and representative transgeniclines transformed with pSZ2299 and pSZ2300 DNA. Sample C10: C12: C14:C16: C18: C18: C18: ID 0 0 0 0 0 1 2 Strain B 4.83 28.54 15.64 12.641.3  27.99 7.75 D1520-A 8.59 35.09 16.55 11.96 1.69 19.49 5.59 D1520-B8.13 33.93 16.46 12.44 1.57 20.66 5.96 D1520-C 7.6  33.1  16.21 12.651.5  21.41 6.48 D1520-D 7.35 32.54 16.03 12.79 1.67 22.16 6.41 D1520-E7.28 32.21 16.2  12.99 1.73 22.39 6.28 D1521-A 6.14 31.5  15.98 12.961.96 22.52 8   D1521-B 6.17 31.38 15.98 12.87 2.08 22.54 7.92 D1521-C5.99 31.31 15.75 12.79 2.23 22.45 8.36 D1521-D 5.95 31.05 15.71 12.842.48 22.69 8.32 D1521-E 5.91 30.58 15.85 13.22 1.97 23.55 7.84

The transgenic CuPSR23 LPAAT2 strains (D1520A-E) show a significantincrease in the accumulation of C10:0, C12:0, and C14:0 fatty acids witha concomitant decrease in C18:1 and C18:2. The transgenic CuPSR23 LPAAT3strains (D1521A-E) show a significant increase in the accumulation ofC10:0, C12:0, and C14:0 fatty acids with a concomitant decrease inC18:1. The expression of the CuPSR23 LPAAT in these transgenic linesappears to be directly responsible for the increased accumulation ofmid-chain fatty acids in general, and especially laurates. While thetransgenic lines show a shift from longer chain fatty acids (C16:0 andabove) to mid-chain fatty acids, the shift is targeted predominantly toC10:0 and C12:0 fatty acids with a slight effect on C14:0 fatty acids.The data presented also show that co-expression of the LPAAT2 and LPAAT3genes from Cuphea PSR23 and the FATB2 from C. wrightii (expressed in thestrain Strain B) have an additive effect on the accumulation of C12:0fatty acids.

Our results suggest that the LPAAT enzymes from Cuphea PSR23 are activein the algal strains derived from UTEX 1435. These results alsodemonstrate that the enzyme functions in conjunction with theheterologous FatB2 acyl-ACP thioesterase enzyme expressed in Strain B,which is derived from Cuphea wrightii.

Example 44 Alteration of Fatty Acid Levels in Strain UTEX1435 by theExpression of Cuphea PSR23 LPAATX in Combination with Cuphea WrightiiFATB2

Here we demonstrate the effect of expression of a1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT) in a previouslydescribed P. moriformis (UTEX 1435) transgenic strain, Strain B. Asdescribed above, Strain B is a transgenic strain expressing the acyl ACPthioesterase (FATB2) from Cuphea wrightii, which accumulates C12:0 fattyacids between 40 to 49%. Further to Example 43, a third CuPSR23 LPAAT,LPAATx, was identified by analysis of a combination of CuPSR23 genomicsequences and transcriptomic sequences derived from seed RNAs.Expression of a mid-chain specific LPAAT should thus increase thepercentage of TAGs that have a capric acid (C10:0 fatty acid), lauricacid (C12:0 fatty acid), or myristic acid (C14:0 fatty acid) at the sn-2position, and should consequently elevate the overall levels of thesefatty acids. In Example 43, LPAAT2 and LPAAT3 were shown to increasecaprate, laurate, and myristate accumulation in strain B. LPAATx wasintroduced into strain B to determine its effect on fatty acid levels inthis strain. The LPAATx gene was codon optimized to reflect UTEX 1435codon usage. Transformations, cell culture, lipid production and fattyacid analysis were all carried out as previously described.

Decreased caprate, laurate, and myristate accumulation and increasedpalmitate and stearate accumulation in strain Strain B by the expressionof the Cuphea PSR23 1-acyl-sn-glycerol-3-phosphate acyltransferase(LPAATx) [pSZ2575]: In this example, transgenic strains were generatedvia transformation of strain B with the construct pSZ2575 encodingCuPSR23 LPAATx. The transgenic strains were selected for resistance tothe antibiotic G418. Construct pSZ2575 can be written aspLOOP5′::CrTUB2:NeoR:CvNR::PmAMT3:CuPSR23LPAATx:CvNR ::pLOOP3′. Thesequence of the transforming DNA is provided below (pSZ2575). Therelevant restriction sites in the construct from 5′-3′, BspQI, KpnI,XbaI, MfeI, BamHI, EcoRI, SpeI, XhoI, SacI, BspQ1, respectively, areindicated in lowercase, bold, and underlined. BspQ1 sites delimit the 5′and 3′ ends of the transforming DNA. Bold, lowercase sequences at the 5′and 3′ end of the construct represent genomic DNA from UTEX 1435 thattarget integration to the pLoop locus via homologous recombination.Proceeding in the 5′ to 3′ direction, the selection cassette has the C.reinhardtii, β-tubulin promoter driving expression of the NeoR gene(conferring resistance to G418) and the Chlorella vulgaris NitrateReductase (NR) gene 3′ UTR. The promoter is indicated by lowercase,boxed text. The initiator ATG and terminator TGA for NeoR are indicatedby uppercase italics, while the coding region is indicated withlowercase italics. The 3′ UTR is indicated by lowercase underlined text.The spacer region between the two cassettes is indicated by upper casetext. The second cassette containing the codon optimized LPAATx gene(pSZ2575) from Cuphea PSR23 is driven by the Prototheca moriformisendogenous AMT3 promoter, and has the same Chlorella vulgaris NitrateReductase (NR) gene 3′ UTR. In this cassette, the AMT3 promoter isindicated by lowercase, boxed text. The initiator ATG and terminator TGAfor the CuPSR23 LPAATx genes are indicated in uppercase italics, whilethe coding region is indicated by lowercase italics. The 3′ UTR isindicated by lowercase underlined text. The final construct wassequenced to ensure correct reading frame and targeting sequences.

104961 pSZ2575 Transforming Construct

(SEQ ID NO: 92)  gctcttccgctaacggaggtctgtcaccaaatggaccccgtctattgcgggaaaccacggcgatggcacgtttcaaaacttgatgaaatacaatattcagtatgtcgcgggcggcgacggcggggagctgatgtcgcgctgggtattgcttaatcgccagcttcgcccccgtcttggcgcgaggcgtgaacaagccgaccgatgtgcacgagcaaatcctgacactagaagggctgactcgcccggcacggctgaattacacaggcttgcaaaaataccagaatttgcacgcaccgtattcgcggtattttgttggacagtgaatagcgatgcggcaatggcttgtggcgttagaaggtgcgacgaaggtggtgccaccactgtgccagccagtcctggcggctcccagggccccgatcaagagccaggacatccaaactacccacagcatcaacgccccggcctatactcgaaccccacttgcactctgcaatggt

cctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatccCGCGTCTCGAACAGAGCGCGCAGAGGAACGCTGAAGGTCTCGCCTCTGTCGCACCTCAGCGCGGCATACACCACAATAACCACCTGACGAATGCGCTTGGTTCTTCGTCCATTAGCGAAGCGTCCGGTTCACACACGTGCCACGTTGGCGAGGTGGCAGGTGACAATGATCGGTGGAGCTGATGG

ctagtATGgagatccccccccactgcctgtgctccccctcccccgccccctcccagctgtactacaagaagaagaagcacgccatcctgcagacccagaccccctaccgctaccgcgtgtcccccacctgcttcgcccccccccgcctgcgcaagcagcacccctaccccctgcccgtgctgtgctaccccaagctgctgcacttctcccagccccgctaccccctggtgcgctcccacctggccgaggccggcgtggcctaccgccccggctacgagctgctgggcaagatccgcggcgtgtgcttctacgccgtgaccgccgccgtggccctgctgctgttccagtgcatgctgctgctgcaccccttcgtgctgctgttcgaccccttcccccgcaaggcccaccacaccatcgccaagctgtggtccatctgctccgtgtccctgttctacaagatccacatcaagggcctggagaacctgccccccccccactcccccgccgtgtacgtgtccaaccaccagtccttcctggacatctacaccctgctgaccctgggccgcaccttcaagttcatctccaagaccgagatcttcctgtaccccatcatcggctgggccatgtacatgctgggcaccatccccctgaagcgcctggactcccgctcccagctggacaccctgaagcgctgcatggacctgatcaagaagggcgcctccgtgttcttcttccccgagggcacccgctccaaggacggcaagctgggcgccttcaagaagggcgccttctccatcgccgccaagtccaaggtgcccgtggtgcccatcaccctgatcggcaccggcaagatcatgccccccggctccgagctgaccgtgaaccccggcaccgtgcaggtgatcatccacaagcccatcgagggctccgacgccgaggccatgtgcaacgaggcccgcgccaccatctcccactccctggacgacTGAttaattaactcgaggcagcagcaptcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagcttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctt gagctcagcggcgacggtcctgctaccgtacgacgttgggcacgcccatgaaagffigtataccgagcttgttgagcgaactgcaagcgcggctcaaggatacttgaactcctggattgatatcggtccaataatggatggaaaatccgaacctcgtgcaagaactgagcaaacctcgttacatggatgcacagtcgccagtccaatgaacattgaagtgagcgaactgttcgcttcggtggcagtactactcaaagaatgagctgctgttaaaaatgcactctcgttctctcaagtgagtggcagatgagtgctcacgccttgcacttcgctgcccgtgtcatgccctgcgccccaaaatttgaaaaaagggatgagattattgggcaatggacgacgtcgtcgctccgggagtcaggaccggcggaaaataagaggcaacacactccgcttctta gctcttcg

To determine the impact of the CuPSR23 LPAATx gene on fatty acidaccumulation, the above construct containing the codon optimized CuPSR23LPAATx gene driven by the UTEX 1453 AMT3 promoter was transformed intostrain B.

Primary transformants were clonally purified and grown under lownitrogen conditions at pH7.0; the strains require growth at pH 7.0 toallow for maximal expression of the CuPSR23 LPAATx and CwFATB2 genesdriven by the pH-regulated AMT3 promoter. The resulting profiles from aset of representative clones arising from these transformations areshown in Table 35, below. D1542 represents clones of Strain B withCuPSR23 LPAATx.

TABLE 35 Fatty acid profiles of Strain B and representative transgeniclines transformed with pSZ2575. Sample ID C10:0 C12:0 C14:0 C16:0 C18:0C18:1 C18:2 Strain 4.77 28.63 15.48 12.65 1.28 28.20 7.57 B D1542- 1.1913.25 10.48 21.34 4.49 32.07 14.78 A D1542- 1.15 14.01 10.62 20.61 3.9932.12 15.24 B D1542- 1.21 13.69 10.83 20.40 3.59 33.54 15.05 C D1542-1.56 16.83 11.51 18.44 2.94 33.97 12.74 D D1542- 2.15 18.58 11.94 18.223.17 32.63 11.62 E

The transgenic CuPSR23 LPAATx strains (D1542A-E) show a significantdecrease in the accumulation of C10:0, C12:0, and C14:0 fatty acidsrelative to the parent, Strain B, with a concomitant increase in C16:0,C18:0, C18:1 and C18:2. The expression of the CuPSR23 LPAATx gene inthese transgenic lines appears to be directly responsible for thedecreased accumulation of mid-chain fatty acids (C10-C14) and theincreased accumulation of C16:0 and C18 fatty acids, with the mostpronounced increase observed in palmitates (C16:0). The data presentedalso show that despite the expression of the midchain specific FATB2from C. wrightii (present in Strain B), the expression of CuPSR23 LPAATxappears to favor incorporation of longer chain fatty acids into TAGs.

Our results suggest that the LPAATx enzyme from Cuphea PSR23 is activein the algal strains derived from UTEX 1435. Contrary to Cuphea PSR23LPAAT2 and LPAAT3, which increase mid-chain fatty acid levels, CuPSR23LPAATx leads to increased C16:0 and C18:0 levels. These resultsdemonstrate that the different LPAATs derived from CuPSR23 (LPAAT2,LPAAT3, and LPAATx) exhibit different fatty acid specificities in StrainB as judged by their effects on overall fatty acid levels.

Example 45 Reduction in Chain Length of Fatty Acid Profile as a Resultof Overexpressing an Endogenous Microalgal FATA Acyl-ACP Thioesterase

Here, we demonstrate that over expression of the Prototheca moriformisendogenous thioesterases FATA1 in UTEX1435 results in a clear diminutionof cell triglyceride C18:0 and C18:1 acyl chains with an increase inC16:0, C14:0.

Constructs used for the over expression of the P. moriformis FATA1 gene(pSZ2422, pSZ2421): To over express the PmFATA1 in P. moriformis STRAINJ, a codon optimized PmFATA1 gene was been transformed into STRAIN J.The Saccharomyces cerevisiae invertase gene was utilized as theselectable marker to confer the ability of growing on sucrose media. Theconstruct pSZ2422 that have been expressed in STRAIN J can be writtenas: 6SA:: CrTUB2-ScSUC2-CvNR3′:PmAMT3-Pm FATA1 (opt)-CvNR3′::6SB, andthe construct pSZ2421 can be written as 6SA::CrTUB2-ScSUC2-CvNR3′:PmAMT3-S106SAD TP-Pm FATA1 (opt)-CvNR3′::6SB.

The sequence of the transforming DNA is provided below. Relevantrestriction sites in the construct pSZ2422 are indicated in lowercase,bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, Mfe I, BamH I,EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I, respectively. BspQI sitesdelimit the 5′ and 3′ ends of the transforming DNA. Bold, lowercasesequences represent genomic DNA from STRAIN J that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene (conferring the abilityof STRAIN J to metabolize sucrose) is indicated by boxed text. Theinitiator ATG and terminator TGA for invertase are indicated byuppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by an endogenous amt03promoter of P. moriformis, indicated by boxed italics text. TheInitiator ATG and terminator TGA codons of the PmFATA1 are indicated byuppercase, bold italics, while the remainder of the gene is indicated bybold italics. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the STRAIN J 6Sgenomic region indicated by bold, lowercase text.

Relevant restriction sites in the construct pSZ2421 are the same aspSZ2422. In pSZ2421, the PmFATA1 is fused to the Chlorellaprotothecoides S106 stearoyl-ACP desaturase transit peptide and thetransit peptide is located between initiator ATG of PmFATA1 and the AscI site.

Nucleotide sequence of transforming DNA contained in pSZ2422

(SEQ ID NO: 93) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcc

cgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaag TGAcaattggcagcagcaptcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatg

acttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgatttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgacctgacctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctc ttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgattcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc  

To determine the impact on fatty acid profiles when the endogenous FATA1gene have been over expressed in STRAIN J, both the P. moriformis FATA1with native transit peptide and PmFATA1 fused to a Chlorellaprotothecoides SAD transit peptide were driven by the amt03 promoter andthe resulting plasmids were transformed independently into STRAIN J.

Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at pH7.0 (all the plasmidsrequire growth at pH 7.0 to allow for maximal PmFATA1 gene expressionwhen driven by the pH regulated amt03 promoter). The resulting profilesfrom representative clones arising from transformations with pSZ2422 andpSZ2421 into STRAIN J are shown in the tables below.

In Table 36, below, the impact of over expressing native PmFATA1 is aclear diminution of C18:1 chain lengths with an increase in C16:0,C14:0, and possibly in C18:0. Considering the protein localization ofprocessing, we also tried the PmFATA1 fused to a Chlorellaprotothecoides stearoyl-ACP desaturase transit peptide. Similar to theresults we observed in the amt03-native PmFATA1 construct, the C16:0 andC14:0 levels are significantly higher than the parental strain J.

TABLE 36 Fatty acid profiles in Strain J and derivative transgenic linestransformed with pSZ2422 DNA. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 pH7; Strain J; T374; 7.69 55.00 4.92 24.94 5.19 D1377-7 96well pH 7;Strain J; T374; 6.39 54.11 5.85 25.91 5.76 D1377-13 96well pH 7; StrainJ; T374; 6.57 53.55 4.68 27.18 5.74 D1377-14 96well pH 7; Strain J;T374; 5.29 49.93 4.24 30.76 7.27 D1377-16 96well pH 7; Strain J; T374;4.76 49.10 4.75 32.36 6.77 D1377-9 96well pH 7; Strain J; T374; 4.2846.06 5.14 35.87 6.69 D1377-19 96well Ctrl-pH 7; Strain J 1.42 27.633.31 57.20 8.00

TABLE 37 Fatty acid profiles in STRAIN J and derivative transgenic linestransformed with pSZ2421 DNA. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 pH7; STRAIN J; T374; 6.76 57.06 4.12 23.66 6.07 D1376-21 96well pH 7;STRAIN J; T374; 6.56 54.62 5.44 25.69 5.64 D1376-22 96well pH 7; STRAINJ; T374; 4.54 48.38 4.27 33.23 7.24 D1376-23 96well pH 7; STRAIN J;T374; 4.48 47.66 4.60 34.28 6.91 D1376-19 96well pH 7; STRAIN J; T374;4.53 47.30 4.67 34.51 6.80 D1376-20 96well pH 7; STRAIN J; T374; 3.5642.70 4.03 39.85 7.52 D1376-17 96well Ctrl-pH 7; STRAIN J 1.42 27.633.31 57.20 8.00

Thus, we conclude that percent myristic and lauric acid levels in thefatty acid profile of a microalgal cell can be increased byoverexpression of a C18-preferring acyl-ACP thioesterase.

Example 46 Cell Oils Suitable for Use as Roll-In Shortenings

The nutritional and functional properties of edible fats have beentraditionally associated with specific chemical compositions andcrystallization conditions. Switching from one oil source to another isusually a difficult task since both the melting behavior and structureof the fat changes dramatically, leading to adverse changes infunctionality. In recent history, we can recall the painful period whenpartially hydrogenated fats were replaced with palm oil and palm oilfractions. We examined how the yield stress, elastic modulus,polymorphism, microstructure and melting profile of two fats with vastlydifferent chemical compositions can be matched. Oil A was produced fromPrototheca moriformis cells expressing an exogenous invertase and anUlmus americana acyl-ACP thioesterase with a Chlorella protothecoidesplastid targeting sequence. Oil B was produced from Protothecamoriformis cells expressing an exogenous invertase and a Cupheahookeriana acyl-ACP thioesterase. Oil A contained greater than 62% (w/w)medium chain fatty acids, or MCT (C8:0-C14:0), 23% (C16:0+C18:0) and 9%C18:1, while Oil B contained less than 2% C8:0-C14:0, 54% (C16:0+C18:0)and 29% C18:1. Oil A was thus a medium chain triglyceride rich fat,while Oil B resembled palm oil. Both oils had a solid fat content of˜45% at 20° C., and very similar SFC versus temperature profiles. DSC(dynamic scanning calorimetry) melting profiles showed two major peakscentered around ˜12-13° C. and ˜28-35° C. Both fats were in thebeta-prime polymorphic form (as determined by X-ray diffraction) anddisplayed asymmetric, elongated crystallite morphology withcharacteristic features. The yield stresses and storage moduli (G′) ofOil A and Oil B were 520-550 Pa, and 7×10⁶ Pa-1.8×10⁷ Pa, respectively.A yield stress in this region suggests a satisfactory plasticity, whichcombined with a high storage modulus makes for an ideal roll-inshortening. Thus, it is possible to alter the chemical composition of afood oil while retaining its lamination functionality.

Other suitable enzymes for use with the cells and methods of any of theabove embodiments of the invention include those that have at least 70%amino acid identity with one of the proteins listed in the descriptionabove and that exhibit the corresponding desired enzymatic activity. Inadditional embodiments, the enzymatic activity is present in a sequencethat has at least about 75%, at least about 80%, at least about 85%, atleast about 90%, at least about 95%, or at least about 99% identity withone of the above described nucleic acid sequences, all of which arehereby incorporated by reference as if fully set forth.

Example 47 Fractionation to Remove Trisaturates from a TailoredMicrobial Oil that is a Cocoa Butter Mimetic

A refined bleached and deodorized oil was obtained from Strain K4 (seeExample 35). The oil was heated to 70° C. and cooled at 0.5° C. per minto 36° C. and held at 36° C. for 1 hour. An approximately 2.5 ml samplewas then centrifuged at 36° C. for 1 hour at 4300. A liquid supernatantwas recovered and analyzed using lipase and mass spectrometry. Thesample was found to be depleted in tristearin (SSS), SSP, and PPS. Thetriacylglycerols of the sample were found to be very similar to that ofcocoa butter and the liquid supernatant was even closer to that of cocoabutter in terms of low amounts of trisaturates. Further fractionationexperiments are described in Example 64.

TABLE 38 TAG profile of oil from the K4 strain before and afterfractionation as compared to cocoa butter. fractionation upper TAG K4oil layer (liquid) cocoa butter OOL (+?) 0.12 0.12 0.00 POL 0.23 0.310.33 PLP 2.41 3.38 1.58 MOP 0.93 1.25 0.00 PPM (+MMS) 0.42 0.29 0.00 OOO0.23 0.34 0.00 SOL 0.36 0.47 0.32 OOP 0.95 1.42 2.44 PLS 5.66 7.90 2.90POP (+MSO) 11.80 15.20 17.93 PPP + MPS 2.22 1.07 0.36 OOS 1.19 1.68 3.02SLS (+PLA) 3.96 5.11 1.77 POS 27.22 32.80 40.25 PPS (+SSM) 6.47 1.520.49 MaOO 0.00 0.00 0.36 SLA 0.31 0.34 0.00 SOS (+POA) 17.84 22.50 24.93SSP (+PPA) 9.24 0.96 0.63 SOA (+POB) 1.39 1.68 1.51 SSS (+PSA) 5.25 0.230.33 SOB + LgOP 0.38 0.44 0.27 SSA 0.41 0.00 0.00 SOLg 0.41 0.00 0.00PSLg + ASB 0.26 0.00 0.00 SOHx 0.12 0.51 0.00 SSLg 0.21 0.14 0.15 SUMarea % 100.00 99.67 99.57

Example 48 Production of High-Stearate Triglyceride Oil in an OleaginousCell by Overexpression of KASII, Knockout of One SAD Allele andRepression of a Second SAD Allele

The oleaginous, non-photosynthetic alga, Prototheca moriformis, storescopious amounts of triacylglyceride oil under conditions where thenutritional carbon supply is in excess, but cell division is inhibiteddue to limitation of other essential nutrients. Bulk biosynthesis offatty acids with carbon chain lengths up to C18 occurs in the plastids;fatty acids are then exported to the endoplasmic reticulum whereelongation past C18 and incorporation into triacylglycerides (TAGs) isbelieved to occur. Lipids are stored in large cytoplasmic organellescalled lipid bodies until environmental conditions change to favorgrowth, whereupon they are rapidly mobilized to provide energy andcarbon molecules for anabolic metabolism. Wild-type P. moriformisstorage lipid is mainly comprised of ˜60% oleic (C18:1), ˜25-30%palmitic (C16:0), and ˜5-8% linoleic (C18:2) acids, with minor amountsof stearic (C18:0), myristic (C14:0), α-linolenic (C18:3α), andpalmitoleic (C16:1) acids. This fatty acid profile results from therelative activities and substrate affinities of the enzymes of theendogenous fatty acid biosynthetic pathway. P. moriformis is amenable tomanipulation of fatty acid and lipid biosynthesis using moleculargenetic tools, enabling the production of oils with fatty acid profilesthat are very different to the wild-type composition. Herein we describestrains where we have modified the expression of stearoyl-ACP desaturase(SAD) and β-ketoacyl-ACP synthase II (KASII) genes in order to generatestrains with up to 57% stearate and as little as 7% palmitate. Weidentify additional strains with up to 55% stearate and as low as 2.4%linoleate when we perform similar modifications in conjunction withdown-regulating the expression of the FATA thioesterase and the FAD2fatty acid desaturase genes.

Soluble SADs are plastid-localized, di-iron enzymes which catalyze thedesaturation of acyl carrier protein (ACP)-bound stearate to oleate(C18:1 cis-Δ⁹). Previously, we have established that hairpin constructstargeting the SAD1 or SAD2 transcripts activate the cellular RNAinterference (RNAi) machinery, down-regulating SAD activity andresulting in elevated levels of C18:0 in the storage lipid. SAD activityis also reduced in strains where we disrupt one of the two alleles ofSAD2, encoding the major SADs that are expressed during storage lipidbiosynthesis. The Fatty Acid Desaturase 2 (FAD2) gene encodes anendoplasmic reticulum membrane-associated desaturase that convertsoleate to linoleate (C18:2 cis-Δ⁹, cis-Δ¹²). Hairpin RNAi constructstargeting FAD2 reduce linoleate levels to 1-2%. KASII is a fatty acidsynthase which specifically catalyzes the condensation of malonyl-ACPwith palmitoyl (C16:0)-ACP to form β-keto-stearoyl-ACP. We have shownthat overexpression of KASII in P. moriformis causes C16:0 levels todecrease with a concomitant increase in C18:1 abundance. In the examplesbelow we demonstrate that by down-regulating SAD gene expression usingRNAi, disrupting an allele of the SAD2 gene, and overexpressing theKASII fatty acid synthase, we generate strains capable of accumulatingstearate in excess of 50% of the total fatty acids, and with SOS as themajor TAG species. SOS levels increase up to 47% in strains whichcombine SAD2 and FAD2 down-regulation with KASII overexpression.

Constructs used for SAD2 knockout/RNAi in S1920: A DNA construct,pSZ2282, was made to simultaneously disrupt the SAD2-1 allele andexpress a SAD2 hairpin construct in Strain J. A Saccharomyces cerevisiaeSUC2 gene, encoding sucrose invertase, which was codon-optimized forexpression in P. moriformis, was utilized as a selectable marker fortransformation. The sequence of the transforming DNA is providedimmediately below. Relevant restriction sites are indicated inlowercase, bold, and are from 5′-3′ BspQI, KpnI, AscI, MfeI, BamHI,AvrII, EcoRV, EcoRI, SpeI, BamHI, HinDIII, and SacI, respectively. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Underlinedsequences at the 5′ and 3′ flanks of the construct represent genomic DNAfrom P. moriformis that enable targeted integration of the transformingDNA via homologous recombination at the SAD2-1 locus. Proceeding in the5′ to 3′ direction, the Chlamydomonas reinhardtii TUB2 promoter drivingthe expression of the Saccharomyces cerevisiae SUC2 gene (encodingsucrose hydrolyzing activity, thereby permitting the strain to grow onsucrose) is indicated by lowercase, boxed text. The initiator ATG andterminator TGA for SUC2 are indicated by uppercase italics, while thecoding region is indicated with lowercase italics. The 3′ UTR of theChlorella vulgaris nitrate reductase (NR) gene is indicated by smallcapitals, followed by a spacer region indicated by lowercase text. Asecond C. reinhardtii TUB2 promoter sequence, indicated by lowercaseboxed text, drives expression of the SAD2 hairpin C sequence. The senseand antisense strands are indicated with uppercase, bold italics, andare separated by the P. moriformis Δ¹²-fatty acid desaturase (FAD2)intron and the first 10 bases of the FAD2 second exon (uppercaseitalics). A second C. vulgaris NR 3′ UTR is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2282:(SEQ ID NO: 94) gctcttcgggtcgccgcgctgcctcgcgtcccctggtggtgcgcgcggtcgccagcgaggccccgctgggcgttccgccctcggtgcagcgcccctcccccgtggtctactccaagctggacaagcagcaccgcctgacgcccgagcgcctggagctggtgcagagcatggggcagtttgcggaggagagggtgctgcccgtgctgcaccccgtggacaagctgtggcagccgcaggactttttgcccgaccccgagtcgcccgacttcgaggatcaggtggcggagctgcgcgcgcgcgccaaggacctgcccgacgagtactttgtggtgctggtgggggacatgatcacggaggaggcgctgccgacctacatggccatgctcaacacgctggacggcgtgcgcgacgacacgggcgcggccgaccacccgtgggcgcgctggacgcggcagtgggtggccgaggagaaccggcacggcgacctgctgaacaagtactgctggctgacggggcgcgtcaacatgcgggccgtggaggtgaccatcaacaacctgatcaagagcggcatgaacccgcagacggacaacaacccttattt

gaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttcacagcctagggatatc

TGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTFCCAG

CAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAAAGCTGgagctccagccacggcaacaccgcgcgccttgcggccgagcacggcgacaagaacctgagcaagatctgcgggctgatcgccagcgacgagggccggcacgagatcgcctacacgcgcatcgtggacgagttcttccgcctcgaccccgagggcgccgtcgccgcctacgccaacatgatgcgcaagcagatcaccatgcccgcgcacctcatggacgacatgggccacggcgaggccaacccgggccgcaacctcttcgccgacttctccgcggtcgccgagaagatcgacgtctacgacgccgaggactactgccgcatcctggagcacctcaacgcgcgctggaaggtggacgagcgccaggtcagcggccaggccgccgcggaccaggagtacgtcctgggcctgccccagcgcttccggaaactcgccgagaagaccgccgccaagcgcaagcgcgtcgcgcgcaggcccgtcgccttctcctggatctccgggcgcgagatcatggtctagggagcgacgagtgtgcgtgcggggctggcgggagtgggacgccctcctcgctcctctctgttctgaacggaacaatcggccaccccgcgctacgcgccacgcatcgagcaacgaagaaaaccccccgatgataggttgcggtggctgccgggatatagatccggccgcacatcaaagggcccctccgccagagaagaagctcctttcccagcagactcct gaagagc

Identification and analysis of SAD2 knockout/knockdown strains:Construct D1283, derived from pSZ2282, was transformed into Strain J.Primary transformants were clonally purified and grown under standardlipid production conditions at pH 5. The resulting fatty acid profilesfrom representative clones arising from transformation with pSZ2282 intoStrain J are summarized in Table 39, below. D1283 transformantsaccumulated up to ˜42% C18:0 at the expense of C18:1, indicating thatSAD activity was significantly reduced in these strains.

TABLE 39 Fatty acid profiles of D1283 [pSZ2282] primary transformants,compared to the wild-type parental strain, Strain J. Strain J D1283-4D1283-7 D1283-19 D1283-27 D1283-40 D1283-24 Fatty C12:0 0.04 0.05 0.060.07 0.06 0.04 0.05 Acid C14:0 1.31 0.92 1.07 1.01 1.08 1.03 0.96 Area %C16:0 26.68 28.23 29.21 27.24 27.67 27.02 27.07 C16:1 0.78 0.05 0.060.08 0.33 0.14 0.12 C17:0 0.11 0.12 0.15 0.10 0.10 0.12 0.13 C18:0 3.1541.98 40.94 34.20 26.26 23.18 22.82 C18:l 59.30 19.37 18.17 26.87 34.7738.74 39.38 C18:2 7.47 6.22 7.43 7.42 7.31 7.25 7.38 C18:3α 0.57 0.931.03 0.75 0.71 0.72 0.51 C20:0 0.32 1.81 1.67 1.75 1.35 1.36 1.23 C20:l0.00 0.10 0.00 0.12 0.00 0.12 0.11 C22:0 0.05 0.17 0.13 0.20 0.16 0.160.15 C24:0 0.00 0.00 0.00 0.10 0.00 0.00 0.00 sum C18 70.49 68.5 67.5769.24 69.05 69.89 70.09 saturates 31.66 73.28 73.23 64.67 56.68 52.9152.41 unsaturates 68.12 26.67 26.69 35.24 43.12 46.97 47.50

In Table 39, Stearate (C18:0) levels greater than the wild-type levelare highlighted with bold text.

The fatty acid profiles of transformants D1283-4 and -7 were determinedto be stable after more than 30 generations of growth in the absence ofselection (growth on sucrose). The performance of selected strains inshake flask assays was then evaluated, and the fatty acid profiles andlipid titers are presented in Table 40, below. Strain X had the highestlevel of C18:0 (˜44%) and the best lipid titer (˜26%) relative to theStrain J parent, and so was selected for further fermentationdevelopment.

TABLE 40 Fatty acid profiles and lipid titers of SAD2 knockout/knock-down strains derived from D1283 primary transformants, compared to thewild-type parental strain, Strain J. Primary T342; D1283-4 T342; D1283-7Strain J S T U V W X Fatty C14:0 1.59 1.61 1.58 1.55 1.81 1.84 1.34 AcidC16:0 30.47 29.41 28.58 29.24 28.77 29.09 28.47 Area % C16:l 0.82 0.050.07 0.05 0.07 0.05 0.06 C17:0 0.10 0.30 0.29 0.28 0.46 0.37 0.19 C18:03.58 42.85 41.86 43.38 39.99 41.41 44.42 C18:l 56.96 13.52 15.55 13.4913.57 12.98 15.64 C18:2 5.50 8.01 7.85 7.65 10.37 9.47 5.72 C18:3α 0.370.78 0.73 0.82 0.95 0.91 0.64 C20:0 0.22 2.06 2.11 2.11 1.98 1.98 2.32C22:0 0.05 0.32 0.34 0.33 0.33 0.32 0.35 C24:0 0.03 0.43 0.42 0.44 0.490.49 0.37 lipid titer 100 12.3 12.6 13.6 6.2 8.2 25.9 (% parent)

In Table 40, Stearate (C18:0) levels greater than the wild-type levelare highlighted with bold text.

We optimized the performance of Strain X in 7-L fermentations, and foundthat we could match the ˜44% C18:0 level obtained in shake flasks, withlipid productivities that were ˜45% of the wild-type parent. The fattyacid profiles and lipid titers of representative strain K-4fermentations are summarized in Table 41, below. Fermentation of StrainX under optimal conditions yielded nearly 44% C18:0, which was similarto the stearate level that accumulated in shake flask assays. Strain Xproduced high C18:0 levels at both flask and 7-L scale and hadacceptable lipid productivity in 7-L fermentations; consequently thisstrain was selected as a base strain for additional modifications aimedat increasing C18:0 accumulation.

TABLE 41 Fatty acid profiles and lipid titers of strain X, compared to acontrol transgenic strain Strain Y. Strain Strain Y K-4 K-4 K-4Fermentation 110088F14 120489F5 120531F8 120580F1 Fatty Acid C14:0 1.471.18 1.15 1.27 Area % C16:0 25.66 28.68 28.38 28.35 C16:1 0.71 0.11 0.090.06 C18:0 3.16 41.63 42.40 43.67 C18:1 62.24 20.78 19.38 17.63 C18:25.90 5.06 5.38 5.58 C18:3α 0.16 0.24 0.25 0.25 C20:0 0.24 1.36 1.99 2.11C22:0 0.05 0.19 0.28 0.31 C24:0 0.05 0.34 0.29 0.31 sum C18 71.46 67.7167.41 67.13 saturates 30.63 73.38 74.49 76.02 unsaturates 69.01 26.1925.10 23.52 total lipid (g/L) 930 383 539 475

In Table 41, Stearate (C18:0) levels greater than the control arehighlighted with bold text. Strain Y contains S. cerevisiae SUC2,encoding sucrose invertase, integrated at the 6S locus, and has a fattyacid profile that is indistinguishable from the Strain J wild-typeparent.

Constructs used for KASII overexpression in Strain K-4: DNA constructpSZ2734 was made to overexpress a codon-optimized P. moriformis KASIIgene in Strain X. The neoR gene from transposon Tn5, conferringresistance to aminoglycoside antibiotics, was used as a selectablemarker for transformation. The sequence of the transforming DNA isprovided immediately below. Relevant restriction sites are indicated inlowercase, bold, and are from 5′-3′ BspQI, KpnI, XbaI, MfeI, BamHI,AvrII, EcoRV, SpeI, AscI, ClaI, BglII, AflII HinDIII and SacI,respectively. BspQI sites delimit the 5′ and 3′ ends of the transformingDNA. Underlined sequences at the 5′ and 3′ flanks of the constructrepresent genomic DNA from P. moriformis that enable targetedintegration of the transforming DNA via homologous recombination at the6S locus. Proceeding in the 5′ to 3′ direction, the C. reinhardtii TUB2promoter driving the expression of neoR (encoding aminoglycosidephosphotransferase activity, thereby permitting the strain to grow onG418) is indicated by lowercase, boxed text. The initiator ATG andterminator TGA for neoR are indicated by uppercase italics, while thecoding region is indicated with lowercase italics. The 3′ UTR of the C.vulgaris NR gene is indicated by small capitals, followed by a spacerregion indicated by lowercase text. The P. moriformis SAD2-2 promotersequence, indicated by boxed text, drives expression of thecodon-optimized P. moriformis KASII gene. The region encoding the KASIIplastid targeting sequence is indicated by uppercase italics. Thesequence that encodes the mature P. moriformis KASII polypeptide isindicated with bold, uppercase italics, while a 3× FLAG epitope encodingsequence is in bold, underlined, uppercase italics. A second C. vulgarisNR 3′ UTR is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2734: (SEQ ID NO: 95) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggtgtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcctgcagagaggacagcagtgcccagccgct

tatcaATGatcgagcaggacggcctccacgccggctcccccgccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttcac

GCAGACCGCCCACCAGCGCCCCCCCACCGAGGGCCACTGCTFCGGCGCCCGCCTGCCCACCGCCTCCC

TGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAaagcttaattaagagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Overexpression of KASII in Strain X: Construct D1653 derived frompSZ2734 was transformed into Strain X as described previously. Primarytransformants were clonally purified and grown under standard lipidproduction conditions at pH 5. The resulting fatty acid profiles fromrepresentative clones arising from transformation of Strain X with D1653are summarized in Table 42, below. Overexpression of KASII in the SAD2knockout/knock-down Strain K-4 background resulted in multiple strainsaccumulating over 50% C18:0 and with substantially reduced levels ofC16:0. We also observed that KASII over-expressing lines had loweroverall ratios of saturated to unsaturated fatty acids compared toStrain X.

TABLE 42 Fatty acid profiles of D1653 [pSZ2734] primary transformants,compared to the Strain X base strain and the wild-type parental strain,Strain J. D165 D165 D165 D165 D165 D165 D165 D165 D165 D165 D165 D165Strain J K-4 3-89 3-10A 3-2B 3-5B 3-7A 3-75 3-90 3-9B 3-72 3-6B 3-823-66 Fatty C12:0  0.04 0.06 0.27 0.13 0.20 0.19 0.24 0.13 0.12 0.27 0.16 0.18  0.25  0.22 Acid C14:0  1.44 1.06 1.55 1.65 1.79 1.67 1.70 1.531.50 1.74 1.57  1.64  1.48  1.56 Area C16:0  29.23 29.83 8.16 11.4510.68 10.11 9.27 11.14 11.08 9.40 9.78  9.95  8.12  8.65 % C16:1  0.880.10 0.04 0.00 0.00 0.00 0.00 0.04 0.04 0.00 0.04  0.00  0.05  0.06C18:0  2.97 40.17 54.25 53.87 53.61 53.46 53.32 53.32 53.15 52.43 52.2051.23 50.52 50.02 C18:1  58.07 20.15 23.52 22.12 22.20 23.48 24.02 22.7323.45 23.94 25.21 26.07 28.00 28.29 C18:2  6.25 5.25 6.75 6.05 6.42 6.256.56 6.19 5.96 6.88 6.28  6.31  6.59  6.31 C18:3α 0.50 0.68 0.79 0.880.78 0.79 0.79 0.85 0.82 0.86 0.78  0.78  0.78  0.83 C20:0  0.22 1.883.21 2.81 3.01 2.91 3.02 2.86 2.77 3.21 2.74  2.80  2.87  2.80 C20:1 0.02 0.07 0.19 0.21 0.34 0.27 0.28 0.12 0.11 0.41 0.14  0.30  0.28  0.26C22:0  0.05 0.26 0.41 0.34 0.40 0.37 0.37 0.36 0.35 0.42 0.36  0.37 0.36  0.37 C24:0  0.04 0.27 0.49 0.38 0.42 0.41 0.45 0.38 0.36 0.460.39  0.37  0.41  0.41 sum C18 67.78 66.24 85.31 82.92 83.01 83.98 84.6983.09 83.38 84.11 84.47 84.39 85.89 85.45 saturates 33.97 73.52 68.3470.63 70.11 69.12 68.37 69.72 69.33 67.93 67.20  

   

   

  unsaturates 65.71 26.23 31.29 29.26 29.74 30.79 31.65 29.93 30.3832.09 32.45  

   

   

 

In Table 42, Stearate (C18:0) levels greater than the wild-type levelare highlighted with bold text. Palmitate (C16:0) levels lower thanStrain X or J are highlighted with bold. For three strains the ratio ofsaturated to unsaturated fatty acids is <2:1; these are highlighted withbold, italicized text.

Stable lines were isolated from the primary transformants shown in Table42. The fatty acid profiles and lipid titers of shake flask cultures arepresented in Table 43, below. The strains accumulated up to 55% C18:0,with as low as 7% C16:0, with comparable lipid titers to the Strain Xparent. The saturates:unsaturates ratios were substantially reducedcompared to Strain X. Strains AU and AV were selected for evaluation in3-L high-density fermentations.

TABLE 43 Shake flask assays of strains derived from D1653, expressingKASII, driven by the PmSAD2-2 promoter, targeted to the 6S locus. 1653-1653- 1653- 1653- D165 Primary 6B 9B 10A 72 3-89 Strain K-4 5664 AU BMBN BO BP BQ BR AV BS Fatty 10:0  .02 .04  .08  .09 .12  .06  .06 .08 .09 .12  .12  .12 Acid 12:0  .04 .09  .28  .29 .35  .20  .20 .23 .26  .32 .32  .33 Area 14:0  .42 .12  .81  .66 .73  .75  .72 .50 .61  .38  .43 .38 % 16:0  5.59 8.56  .39  .61 .44  .98 0.11 .26 .95  .81  .21  .6316:1  .03 .10  .06  .05 .06  .06  .06 .04 .04  .03  .03  .03 18:0  .600.13 7.60 2.47 5.12 0.25 9.73 4.56 4.01 2.96 3.68 2.12 18:1  2.08 0.747.78 3.93 1.31 5.37 5.70 2.86 2.87 4.37 3.99 5.17 18:2  .16 .83  .98 .52 .72  .55  .64 .20 .24  .11  .83  .04 18:3α .40 .89  .21  .22 .49 .17  .07 .20 .29  .28  .24  .31 20:0  .18 .82  .62  .93 .75  .65  .66.97 .72  .43  .10  .59 20:1  .04 .13  .37  .36 .39  .34  .34 .35 .34 .48  .41  .47 20:1  .07 .00  .00  .00 .00  .00  .00 .00 .00  .00  .00 .00 20:1  .15 .08  .11  .09 .11  .10  .10 .09 .10  .12  .10  .12 22:0 .02 .20  .28  .30 .24  .29  .28 .30 .27  .32  .29  .35 24:0  .00 .03 .16  .29 .00  .03  .15 .16 .02  .05  .04  .07 Sum C18 1.23 7.58 4.575.13 5.63 4.34 4.13 5.81 5.40 6.71 6.73 6.63 Saturates 9.86 1.97  

   

  8.74  

   

  8.05 7.90  

   

   

  Unsaturates 9.91 7.76  

   

  1.07  

   

  1.73 1.87  

   

   

 

In Table 43, Strain X is the parent strain; Strain J is the wild-typebase strain. Stearate (C18:0) levels at least two-fold higher than inthe wild-type strain are highlighted in bold. Palmitate levels that areless than in Strain J and Strain K-4 are highlighted bold. Bold italicsindicate that the saturates:unsaturates ratio is <2:1.

The fatty acid profiles and performance metrics of strains AU and AV aredetailed in Table 44, below. The fatty acid profile of the parent strainX, grown under the same fermentation conditions, is presented forcomparison. The strains that over-express KASII accumulate about 11%more C18:0 than the strain K-4 parent. C16:0 is reduced to 7-9%, andlevels of unsaturated fatty acids increase by 4-5%. The lipid titers ofStrain AU and AV were comparable to K-4, indicating that KASIIover-expression did not have deleterious effects on lipid production.

TABLE 44 End point fatty acid profiles of biomass from strain X, AU andAV fermentations. Strain K-4 AU AV Fermentation 120580F1 130097F3130098F4 pH 5 5 5 C14:0 1.27 1.50 1.35 C16:0 28.35 8.88 7.33 C16:1 0.060.02 0.03 C18:0 43.67 56.88 57.24 C18:1 17.63 21.57 21.66 C18:2 5.586.06 6.94 C18:3α 0.25 0.29 0.22 C20:0 2.11 3.28 3.46 C22:0 0.31 0.400.40 C24:0 0.31 0.37 0.40 sum C18 67.13 84.80 86.06 saturates 76.0271.31 70.18 unsaturates 23.52 27.94 28.85 total lipid (g/L) 475 529 418

The fermentations were cultured for 6 days using a fed-batch process.The Strain X fatty acid profile from fermentation 120580F1 was presentedin Table 41, and is shown again in Table 44 for comparison with StrainsAU and AV. All fermentations were carried out at 32° C., pH 5, 30%dissolved oxygen (DO), 300 mM nitrogen [N], and 557.5 μM iron. The sugarsource was 70% sucrose (S70). Stearate (C18:0) levels higher than in thewild-type strain are indicated with bold. Palmitate (C16:0) levels thatare less than in the wild-type are highlighted bold.

Lab scale oils were prepared from biomass derived from the shake flasksand fermentations described above. The TAG compositions of these oilswere determined by LC/MS. SOS is the major TAG species in both Strain AUand AV, ranging from 33-35% in the biomass from shake flasks, andreaching 37% in the high-density fermentation biomass. The majorpalmitate-containing TAGs are substantially reduced, and trisaturatelevels are less than half of those observed in Strain X oils. Theseresults demonstrate that KASII over-expression in a high-stearatebackground significantly improves SOS accumulation, and reduces theaccumulation of trisaturated TAGs.

Constructs used for FATA-1 disruption, KASII over-expression and FAD2RNAi in Strain J: A DNA construct, pSZ2419, was made to simultaneouslydisrupt the FATA-1 allele, over-express P. moriformis KASII and expressa FAD2 hairpin construct in Strain J. A version of the S. cerevisiaeSUC2 gene, encoding sucrose invertase, which was codon-optimized forexpression in P. moriformis, was utilized as a selectable marker fortransformation. The sequence of the transforming DNA is providedimmediately below. Relevant restriction sites are indicated inlowercase, bold, and are from 5′-3′ BspQI, KpnI, AscI, MfeI, BamHI,AvrII, EcoRV, EcoRI, SpeI, AscI, ClaI, BglII, AflII, HinDIII, SacI,SpeI, and XhoI, respectively. BspQI sites delimit the 5′ and 3′ ends ofthe transforming DNA. Underlined sequences at the 5′ and 3′ flanks ofthe construct represent genomic DNA from P. moriformis that enabletargeted integration of the transforming DNA via homologousrecombination at the FATA-1 locus. Proceeding in the 5′ to 3′ direction,the C. reinhardtii TUB2 promoter driving the expression of the S.cerevisiae SUC2 gene (encoding sucrose hydrolyzing activity, therebypermitting the strain to grow on sucrose) is indicated by lowercase,boxed text. The initiator ATG and terminator TGA for SUC2 are indicatedby uppercase italics, while the coding region is indicated withlowercase italics. The 3′ UTR of the C. vulgaris nitrate reductase (NR)gene is indicated by small capitals, followed by a spacer regionindicated by lowercase text. The P. moriformis AMT3 promoter, indicatedby lowercase boxed text, drives expression of the P. moriformis KASIIgene. The region encoding the plastid targeting peptide from Chlorellaprotothecoides SAD1 is indicated by uppercase italics. The sequence thatencodes the mature P. moriformis KASII polypeptide is indicated withbold, uppercase italics, while a 3× FLAG epitope encoding sequence is inbold, underlined, uppercase italics. A second C. vulgaris NR 3′ UTR isindicated by small capitals. A second C. reinhardtii TUB2 promotersequence, indicated by lowercase boxed text, drives expression of the P.moriformis FAD2 hairpin A sequence. The sense and antisense strands areindicated with uppercase, bold italics, and are separated by the FAD2intron and the first 10 bases of the FAD2 second exon (uppercaseitalics). A third C. vulgaris NR 3′ UTR is indicated by small capitals,followed by a second spacer region that is indicated by lowercase text.

Nucleotide sequence of the transforming DNA from pSZ2419: (SEQ ID NO: 96)  gctcttcggagtcactgtgccactgagttcgactggtagctgaatggagtcgctgctccactaaacgaattgtcagcaccgccagccggccgaggacccgagtcatagcgagggtagtagcgcgccatggcaccgaccagcctgcttgccagtactggcgtctcttccgcttctctgtggtcctctgcgcgctccagcgcgtgcgcttttccggtggatcatgcggtccgtggcgcaccgcagcggccgctgcccatgcagcgccgctgcttccgaacagtggcggtcagggccgcacccgcggtagccgtccgtccggaacccgcccaagagttttgggagcagcttgagccctgcaagatggcggaggacaagcgcatcttcctggaggagcaccggtgcgtggaggtccggggctgaccggccgtcgcattcaacgtaatcaatcgcatgatgatcagaggacacgaagtcttggtggcggtggccagaaacactgtccattgcaagggcatagggatgcgttccttcacctctcatttctcatttctgaatccctccctgctcactctttctcctcctccttcccgttcacgcagcattcggggtacc

ggccggcttcgccgccaagatcagcgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtgg

TTTCTCGGCGTFCAATGCCCGCTGCGGCGACCTGCGTCGCTCGGCGGGCTCCGGGCCCCGGCGCCCA

GTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGA

GCCCGTATTGAGGTCCTGGTGGCGCGCATGGAGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCT

GCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAaagctgtattgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaagacagggtggttggctggatggggaaacgctggtcgcgggattcgatcctgctgcttatatcctccctggaagcacacccacgactctgaagaagaaaacgtgcacacacacaacccaaccggccgaatatttgcttccttatcccgggtccaagagagactgcgatgcccccctcaatcagcatcctcctccctgccgcttcaatcttccctgcttgcctgcgcccgcggtgcgccgtctgcccgcccagtcagtcactcctgcacaggccccttgtgcgcagtgctcctgtaccctttaccgctccttccattctgcgaggccccctattgaatgtattcgttgcctgtgtggccaagcgggctgctgggcgcgccgccgtcgggcagtgctcggcgactttggcggaagccgattgttcttctgtaagccacgcgcttgctgctttgggaagagaagggggggggtactgaatggatgaggaggagaaggaggggtattggtattatctgagttgggt gaagagc

Identification and analysis of FATA-1 knockout, KASII over-expressionand FAD2 RNAi strains: Construct D1358, derived from pSZ2419, wastransformed into Strain J as described previously. Primary transformantswere clonally purified and grown under standard lipid productionconditions at pH 5. The resulting fatty acid profiles fromrepresentative clones arising from transformation of Strain J with D1358are summarized in Table 45, below. The P. moriformis AMT3 promoter isrepressed at pH 5 so the observed phenotypes did not reflectover-expression of P. moriformis KASII. Nevertheless, we observed thatmultiple strains had substantially reduced levels of C16:0 and 10-15%increases in C18:1, suggesting that the construct had disrupted theFATA-1 target gene, increasing the amount of palmitoyl-ACP available forextension by endogenous KASII. One line, D1358-13, was selected forfurther analysis. D1358-13 accumulated ˜17% C16:0, ˜75% C18:1 and lessthan 2% C18:2, indicating that we had successfully integrated at FATA-1and down-regulated activity of the FAD2 Δ¹²-desaturase in this strain.

TABLE 45 Fatty acid profiles of D1358 [pSZ2419] primary transformants,compared to the wild-type parental strain, Strain J. Strain J D1358-13D1358-19 D1358-11 D1358-9 D1358-30 D1358-28 D1358-6 D1358-8 D1358-10D1358-3 Fatty C12:0 0.05 0.08 0.06 0.08 0.06 0.07 0.07 0.09 0.07 0.080.10 Acid C14:0 1.32 0.79 0.83 0.85 0.87 0.84 0.91 0.86 0.89 0.92 0.60Area C16:0 26.66 17.43 18.84 20.03 16.27 18.4 19.1 18.18 15.6 16.4211.24 % C16:1 0.84 0.74 0.79 0.97 0.60 0.77 1.17 0.75 0.56 0.61 0.57C18:0 3.10 2.87 2.97 2.36 3.20 2.67 2.10 2.82 3.22 3.19 2.30 C18:1 59.0774.78 69.54 68.78 71.48 69.55 69.02 68.93 70.44 69.64 75.27 C18:2 7.391.97 5.47 5.61 6.22 6.31 6.42 6.8 7.68 7.78 8.51 C18:3 α 0.55 0.23 0.590.51 0.26 0.39 0.46 0.38 0.24 0.27 0.24 C20:0 0.24 0.22 0.20 0.13 0.320.20 0.03 0.20 0.33 0.31 0.22 C20:1 0.11 0.40 0.29 0.37 0.23 0.33 0.330.39 0.36 0.27 0.40 C22:0 0.11 0.09 0.08 0.07 0.09 0.08 0.08 0.08 0.090.11 0.11 sum C18 70.11 79.85 78.57 77.26 81.16 78.92 78.00 78.93 81.5880.88 86.32 saturates 31.48 21.48 22.98 23.52 20.81 22.26 22.29 22.2320.20 21.03 14.57 unsaturates 67.96 78.12 76.68 76.24 78.79 77.35 77.477.25 79.28 78.57 84.99

In Table 45, Oleate (C18:1) levels greater than the wild-type level arehighlighted with bold text. Palmitate (C16:0) levels less than thewild-type are highlighted with bold text. Levels of linoleate (C18:2)reduced by 1% or more compared to the Strain J parent are highlightedwith bold text.

The fatty acid profiles of strains derived from transformant D1358-13were determined to be stable after more than 60 generations of growth inthe absence of selection (growth on sucrose). The performance ofselected strains in shake flask assays was then evaluated, and the fattyacid profiles and lipid titers are presented in Table 46, below. Flaskexperiments were performed at pH 7, enabling activation of the PmAMT3promoter driving expression of the KASII transgene. The combination ofKASII over-expression and FATA-1 knockout leads to further reductions inpalmitate levels and enhanced oleate accumulation compared to thephenotypes observed at pH 5 (Table 45). With more than 82% C18:1, lessthan 11% C16:0, less than 2% C18:2 and ˜83% of the wild-type lipidtiter, Strain AA was determined to be the most appropriate strain fromthis set to serve as a host strain for subsequent modifications toelevate stearate levels. DNA blot analysis showed that S5003 has asimple insertion of construct D1358 [pSZ2419] at the FATA-1 locus.

TABLE 46 Fatty acid profiles and lipid titers of FATA-1 knockout, KASIIover- expressing, FAD2 RNAi lines derived from D1358-13 primarytransformants, compared to the wild-type parental strain, Strain J.Primary T389; D1358-13 Strain J AA AB AC AD AE AF AG AH AI AJ AK AL AMFatty C12:0 0.05 0.08 0.09 0.11 0.19 0.11 0.14 0.10 0.12 0.08 0.11  0.09 0.20  0.20 Acid C14:0 1.34 0.96 0.98 1.03 1.04 0.96 1.02 0.98 1.03 0.981.01  1.00  1.03  1.02 Area C16:0 29.69 10.72 10.47 8.90 6.99 9.53 9.2710.13 8.99 10.76 9.58 10.00  6.64  6.38 % C16:1 0.88 0.42 0.39 0.31 0.290.39 0.37 0.41 0.32 0.40 0.35  0.35  0.27  0.27 C18:0 2.78 2.92 3.003.16 2.71 2.88 2.85 2.91 3.21 3.03 3.10  3.20  2.77  2.71 C18:1 58.4582.08 82.24 83.66 85.49 83.28 83.38 82.57 83.51 82.12 83.10 82.63 85.8886.13 C18:2 5.83 1.89 1.88 1.80 2.01 1.83 1.89 1.89 1.77 1.73 1.75  1.76 1.94  1.96 C18:3α 0.42 0.23 0.23 0.25 0.35 0.27 0.29 0.27 0.25 0.220.24  0.23  0.34  0.36 C20:0 0.17 0.15 0.16 0.17 0.15 0.15 0.16 0.160.17 0.14 0.16  0.16  0.15  0.15 C20:1 0.05 0.23 0.24 0.27 0.36 0.280.29 0.26 0.27 0.21 0.25  0.24  0.38  0.39 sum C18 67.48 87.12 87.3588.87 90.56 88.26 88.41 87.64 88.74 87.10 88.19 87.82 90.93 91.16saturates 34.03 14.83 14.70 13.37 11.08 13.63 13.44 14.28 13.52 14.9913.96 14.45 10.79 10.46 unsaturates 65.63 84.85 84.98 86.29 88.50 86.0586.22 85.40 86.12 84.68 85.69 85.21 88.81 89.11 lipid titer 100.0 82.881.1 72.8 54.4 68.3 63.7 70.6 72.2 106.9 76.5 77.5  56.7  54.6  (%parent)

In Table 46, Stearate (C18:1) levels greater than the wild-type levelare highlighted with bold text. Palmitate (C16:0) levels lower than thewild-type are highlighted with bold text. Linoleate (C18:2) levels thatare lower than the wild-type are indicated with bold text.

Constructs used for SAD2 knockout/RNAi in S5003: Two DNA constructs,pSZ2283 and pSZ2697, were made to simultaneously disrupt the SAD2-1allele and express a SAD2 hairpin construct in Strain AA. In eachconstruct, the neoR gene from transposon Tn5, conferring resistance toaminoglycoside antibiotics, was used as a selectable marker fortransformation. The sequence of the transforming DNA derived frompSZ2283 is provided immediately below. Relevant restriction sites areindicated in lowercase, bold, and are from 5′-3′ BspQI, KpnI, XbaI,MfeI, BamHI, AvrII, EcoRV, EcoRI, SpeI, BamHI, HinDIII, and SacI,respectively. BspQI sites delimit the 5′ and 3′ ends of the transformingDNA. Underlined sequences at the 5′ and 3′ flanks of the constructrepresent genomic DNA from P. moriformis that enable targetedintegration of the transforming DNA via homologous recombination at theSAD2-1 locus. Proceeding in the 5′ to 3′ direction, the Chlamydomonasreinhardtii TUB2 promoter driving the expression of neoR (encodingaminoglycoside phosphotransferase activity, thereby permitting thestrain to grow on G418) is indicated by lowercase, boxed text. Theinitiator ATG and terminator TGA for neoR are indicated by uppercaseitalics, while the coding region is indicated with lowercase italics.The 3′ UTR of the C. vulgaris NR gene is indicated by small capitals,followed by a spacer region indicated by lowercase text. A second C.reinhardtii TUB2 promoter sequence, indicated by lowercase boxed text,drives expression of the SAD2 hairpin C sequence. The sense andantisense strands are indicated with uppercase, bold italics, and areseparated by the P. moriformis FAD2 intron and the first 10 bases of theFAD2 second exon (uppercase italics). A second C. vulgaris NR 3′ UTR isindicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2283: (SEQ ID NO: 97) gctcttcgggtcgccgcgctgcctcgcgtcccctggtggtgcgcgcggtcgccagcgaggccccgctgggcgttccgccctcggtgcagcgcccctcccccgtggtctactccaagctggacaagcagcaccgcctgacgcccgagcgcctggagctggtgcagagcatggggcagtttgcggaggagagggtgctgcccgtgctgcaccccgtggacaagctgtggcagccgcaggactttttgcccgaccccgagtcgcccgacttcgaggatcaggtggcggagctgcgcgcgcgcgccaaggacctgcccgacgagtactttgtggtgctggtgggggacatgatcacggaggaggcgctgccgacctacatggccatgctcaacacgctggacggcgtgcgcgacgacacgggcgcggccgaccacccgtgggcgcgctggacgcggcagtgggtggccgaggagaaccggcacggcgacctgctgaacaagtactgctggctgacggggcgcgtcaacatgcgggccgtggaggtgaccatcaacaacctgatcaagagcggcatgaacccgcagacggacaacaacccttattt

ggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtgg

GTTTTGGTTGCCCGTATCGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACC

GTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAaagctggagctccagccacggcaacaccgcgcgccttgcggccgagcacggcgacaagaacctgagcaagatctgcgggctgatcgccagcgacgagggccggcacgagatcgcctacacgcgcatcgtggacgagttcttccgcctcgaccccgagggcgccgtcgccgcctacgccaacatgatgcgcaagcagatcaccatgcccgcgcacctcatggacgacatgggccacggcgaggccaacccgggccgcaacctcttcgccgacttctccgcggtcgccgagaagatcgacgtctacgacgccgaggactactgccgcatcctggagcacctcaacgcgcgctggaaggtggacgagcgccaggtcagcggccaggccgccgcggaccaggagtacgtcctgggcctgccccagcgcttccggaaactcgccgagaagaccgccgccaagcgcaagcgcgtcgcgcgcaggcccgtcgccttctcctggatctccgggcgcgagatcatggtctagggagcgacgagtgtgcgtgcggggctggcgggagtgggacgccctcctcgctcctctctgttctgaacggaacaatcggccaccccgcgctacgcgccacgcatcgagcaacgaagaaaaccccccgatgataggttgcggtggctgccgggatatagatccggccgcacatcaaagggcccctccgccagagaagaagctcctttcccagcagactcctgaag agc

The sequence of the transforming DNA derived from pSZ2697 is providedimmediately below. Relevant restriction sites are indicated inlowercase, bold, and are from 5′-3′ NsiI, SpeI, BamHI, HinDIII, SacII,EcoRV, KpnI, XbaI, MfeI, BamHI, AvrII, EcoRV, EcoRI and XbaI,respectively. Underlined sequences at the 5′ and 3′ flanks of theconstruct represent genomic DNA from P. moriformis that enable targetedintegration of the transforming DNA via homologous recombination at theSAD2-1 locus. Proceeding in the 5′ to 3′ direction, the SAD2 hairpin Csense and antisense strands are indicated with uppercase, bold italics,and are separated by the P. moriformis FAD2 intron and the first 10bases of the FAD2 second exon (uppercase italics). The 3′ UTR of the C.vulgaris NR gene is indicated by small capitals. The Chlorellasorokiniana Glutamate Dehydrogenase (GDH) promoter, driving theexpression of neoR (encoding aminoglycoside phosphotransferase activity,thereby permitting the strain to grow on G418) is indicated bylowercase, boxed text. The initiator ATG and terminator TGA for neoR areindicated by uppercase italics, while the coding region is indicatedwith lowercase italics. A second C. vulgaris NR 3′ UTR is indicated bysmall capitals, followed by a spacer region indicated by lowercase text.

Nucleotide sequence of the transforming DNA from pSZ2697:(SEQ ID NO: 98) atgcatgccggtcaccacccgcatgctcgtactacagcgcacgcaccgcttcgtgatccaccgggtgaacgtagtcctcgacggaaacatctggttcgggcctcctgcttgcactcccgcccatgccgacaacctttctgctgttaccacgacccacaatgcaacgcgacacgaccgtgtgggactgatcggttcactgcacctgcatgcaattgtcacaagcgcttactccaattgtattcgtttgttttctgggagcagttgctcgaccgcccgcgtcccgcaggcagcgatgacgtgtgcgtggcctgggtgtttcgtcgaaaggccagcaaccctaaatcgcaggcgatccggagattgggatctgatccgagtttggaccagatccgccccgatgcggcacgggaactgcatcgactcggcgcggaacccagctttcgtaaatgccagattggtgtccgatacctggatttgccatcagcgaaacaagacttcagcagcgagcgtatttggcgggcgtgctaccagggttgcatacattgcccatttctgtctggaccgctttactggcgcagagggtgagttgatggggttggcaggcatcgaaacgcgcgtgcatggtgtgcgtgtctgttttcggctgcacgaattcaatagtcggatgggcgacggtagaattgggtgtggcgctcgcgtgcatgcctcgccccgtcgggtgtcatgaccgggactggaatcccccctcgcgaccatcttgctaacgctcccgactctcccgactagt

GCCCGTATCGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCT

GACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAA

tagaatatcaATGatcgagcaggacggcctccacgccggctcccccgccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttcacagcctagggatatcgaattccgggtcgccgcgctgcctcgcgtcccctggtggtgcgcgcggtcgccagcgaggccccgctgggcgttccgccctcggtgcagcgcccctcccccgtggtctactccaagctggacaagcagcaccgcctgacgcccgagcgcctggagctggtgcagagcatggggcagtttgcggaggagagggtgctgcccgtgctgcaccccgtggacaagctgtggcagccgcaggactttttgcccgaccccgagtcgcccgacttcgaggatcaggtggcggagctgcgcgcgcgcgccaaggacctgcccgacgagtactttgtggtgctggtgggggacatgatcacggaggaggcgctgccgacctacatggccatgctcaacacgctggacggcgtgcgcgacgacacgggcgcggccgaccacccgtgggcgcgctggacgcggcagtgggtggccgaggagaaccggcacggcgacctgctgaacaagtactgctggctgacggggcgcgtcaacatgcgggccgtggaggtgaccatcaacaacctgatcaagagcggcatgaacccgcagacggacaacaacccttatttggggttcgtctacacctccttccaggagcgcgccaccaagta tctaga

Identification and analysis of SAD2 knockout/knockdown strains in theS5003 background: Constructs D1639, derived from pSZ2697, and D1682,derived from pSZ2283, were transformed into Strain AA as describedpreviously. Primary transformants were clonally purified and grown understandard lipid production conditions at pH 7. The resulting fatty acidprofiles from representative clones arising from transformation aresummarized in Table 47, below. D1639 transformants accumulated up to 56%C18:0, and D1682 transformants accumulated a maximum of about 35% C18:0.Most of the increases in stearate came at the expense of C18:1,indicating that SAD activity was significantly reduced by the SAD2knockout/RNAi constructs in these strains. C16:0 levels varied from 6%to 14%; C18:2 ranged from 2-5%. Most strains maintained the low C16:0and C18:2 phenotypes of the Strain AA parent. These fatty acid profilesdemonstrate that down-regulating SAD2 expression using knockout/RNAiconstructs, in a background with disrupted FATA-1, KASII over-expressionand FAD2 RNAi, produces strains with high C18:0, low C16:0 and low C18:2phenotypes. These strains will be useful for production of highstability, high stearate, high oleic oils, and oils which have high SOScontent.

TABLE 47 Fatty acid profiles of D1639 [pSZ2697] and D1682 [pSZ2283]primary transformants, compared to the wild-type strain, Strain J, andthe Strain AA parental base strain. Strain J AA D1682-4 D1682-17 D1682-7D1682-6 D1639-2 D1639-5 D1639-10 D1639-19 Fatty C12:0 0.04 0.11 0.140.10 0.32 0.31 0.00 0.19 0.17 0.00 Acid C14:0 1.29 0.98 1.03 0.94 1.111.15 1.64 1.39 1.61 1.02 Area C16:0 27.50 7.75 8.68 10.41 5.70 5.96 7.549.90 14.39 12.02 % C16:1 0.71 0.30 0.06 0.07 0.07 0.10 0.00 0.00 0.000.00 C18:0 3.28 3.60 35.46 29.92 24.66 22.30 55.96 53.38 43.46 37.30C18:1 57.80 84.14 48.39 52.49 61.04 63.60 23.70 26.79 32.93 42.81 C18:27.90 2.09 2.37 2.36 3.03 2.88 5.09 3.50 3.22 2.79 C18:3 α 0.57 0.32 0.500.65 0.66 0.58 1.59 0.98 1.01 0.85 C20:0 0.28 0.23 2.07 1.87 1.75 1.513.04 2.73 2.29 2.22 C20:1 0.18 0.35 0.54 0.49 0.78 0.83 0.37 0.33 0.300.40 C22:0 0.06 0.02 0.27 0.27 0.23 0.20 0.43 0.36 0.29 0.29 C24:0 0.090.02 0.33 0.26 0.34 0.26 0.64 0.45 0.32 0.31 sum C18 69.55 90.14 86.7285.42 89.39 89.36 86.34 84.65 80.62 83.75 saturates 32.54 12.70 47.9843.77 34.11 31.69 69.25 68.40 62.53 53.16 unsaturates 67.16 87.21 51.8656.06 65.58 67.99 30.75 31.60 37.46 46.85

In Table 47, Stearate (C18:0) levels greater than the wild-type levelare highlighted with bold text. Oleate (C18:1) levels that are higherthan in the wild-type are indicated with bold text. Palmitate (C16:0)levels less than the wild-type level are highlighted with bold. Reducedlevels of linoleate (C18:2) compared to the wild-type are highlightedwith bold text.

Stable lines were isolated from a number of D1639 and D1682transformants. Shake flask assays were carried out to evaluate theperformance of four lines derived from D1639-5. Fatty acid profiles andrelative lipid titers from the biomass are shown in Table 48, below.

TABLE 48 Shake flask assays of strains derived from D1639-5, expressingSAD2hpC, driven by the CrTUB2 promoter, targeted to the SAD2-1 locus.Primary T530; D1639-5 Strain J AA AW AX AY BL Fatty C10:0 0.01 0.00 0.070.08 0.05 0.04 Acid C12:0 0.02 0.11 0.19 0.22 0.25 0.23 Area % C14:01.52 1.10 1.35 1.32 1.30 1.43 C16:0 31.61 9.59 9.28 8.44 7.74 9.46 C16:11.04 0.34 0.03 0.02 0.01 0.01 C17:0 0.10 0.11 0.10 0.10 0.10 0.09 C18:02.98 4.36 53.01 53.52 55.32 52.09 C18:1 54.81 80.84 27.26 27.52 27.4228.06 C18:2 6.88 2.42 3.55 3.52 2.38 3.45 C18:3α 0.53 0.33 0.97 1.030.82 1.06 C20:0 0.26 0.31 2.88 2.94 3.15 2.72 C20:1 0.05 0.34 0.38 0.380.40 0.37 C22:0 0.03 0.06 0.36 0.37 0.39 0.35 C24:0 0.07 0.08 0.53 0.540.53 0.60 sum C18 65.19 87.95 84.79 85.58 85.94 84.66 saturates 36.5915.70 67.76 67.52 68.82 66.99 unsaturates 63.30 84.26 32.19 32.46 31.0232.95 % wild-type 100.0 70.3 34.8 33.7 31.4 35.3 lipid titer

In Table 48, Strain AA is the parent strain; Strain J is the wild-typebase strain. Stearate (C18:0) levels higher than in the wild-type strainare indicated with bold. Bold text indicates the increased level ofoleate (C18:1) in Strain AA compared to the wild-type. Palmitate (C16:0)levels that are less than in the wild-type are highlighted bold.Linoleate (C18:2) levels that are less than in the wild-type areindicated with bold.

Lab scale oils were prepared from biomass collected from the Strain AW,AX and AY shake flasks. The TAG compositions of these oils weredetermined by LC/MS, and are shown in FIG. 21. SOS accumulation rangedfrom 42-47% in these strains. POS was the next most abundant TAG, at16-17%. Linoleate-containing TAGs were reduced by more than 50% comparedto the Strain AU and AV oils, described above. Strain AW,AX, and AY oilscontained 12-13% trisaturated TAGs (S-S-S), similar to the amounts thataccumulated in the Strain AU and AX oils. Modulation of SAD activityduring oil production to prevent overproduction of saturated fatty acidsmay help to reduce accumulation of trisaturates.

Example 49 Properties of Methyl Oleate from High Oleic Microalgal Oils

Esterified oils high in methyl oleate are useful in a variety ofapplications such as cleaning and lubrication of machinery. For some ofthese applications, high thermal stability is desired. Thermal stabilitytesting was performed on methylated oil prepared from high-oleic andhigh-stability-high oleic triglyceride oils prepared fromheterotrophically grown oleaginous microalgae as described above. Theoils were bleached and deodorized prior to methylation. Commerciallyavailable soya methyl ester was used as a control.

High Oleic (HO) oil was prepared from a high oil-yielding strain ofPrototheca moriformis transformed with a plasmid that can be describedas FatA_Btub:inv:nr::amt03-CwTE2:nr_FatA1. This plasmid was designed tohomologously recombine in the FATA1 chromosomal site, thus ablating aFATA acyl-ACP thioesterase chromosomal allele, while expressing anexogenous acyl-ACP thioesterase from Cuphea wrightii (CwTE2, SEQ ID NO:11) under control of the pH-regulatable amt3 promoter. The CwTE2 genecan be downregulated by cultivation at pH 5 during oil production tofurther elevate oleate production. Sucrose invertase was also expressedas a selection marker and to allow for cultivation of the strain onsucrose as a sole carbon source. The 3′ UTR sequences are from theChlorella vulgaris nitrate reductase gene. The resulting HO strain isdenoted Stain Q. The fatty acid profile of the oil produced by Strain Qis listed below in Table 49.

TABLE 49 Fatty acid profile of high oleic oil from Strain Q. Fatty AcidArea % C10 0.01 C12:0 0.03 C14:0 0.43 C15:0 0.03 C16:0 7.27 C16:1 iso0.81 C16:1  0.689 C17:0 0.06 C18:0  1.198 C18:1 80.15  C18:1 iso 0.08C18:2 8.38 C18:3 ALPHA 0.25 C20:0 0.02 C20:1 0.38 C22:0 0.04 C24:0 0.03

A high-stability-high-oleic oil (HSAO) was also prepared from a highoil-yielding strain of Prototheca moriformis transformed with a plasmidthat can be described as FADc5′_0Btub:inv:nr::btub-CpSAD_CtOTE:nr_FADc3′. The resulting strain (Strain R)expresses sucrose invertase as a selectable marker and to allow forcultivation on sucrose as a sole carbon source. In addition, a FADallele (encoding fatty acid desaturase responsible for the conversion ofoleate to linoleate) is disrupted and an oleate-specific acyl-ACPthioesterase (Carthamus tinctorius OTE, see example 5) fused to thetransit peptide from the SAD gene of Chlorella protothecoides isexpressed under control of the beta tubulin promoter. The 3′ UTRsequences are from the Chlorella vulgaris nitrate reductase gene. Thefatty acid profile of the oil produced by Strain R after heterotrophiccultivation is listed below in Table 50. The fatty acid profile hasgreater than 85% oleate yet almost none of the major polyunsaturates,linoleic and linolenic acids.

TABLE 50 Fatty acid profile of high oleic oil from Strain R. Fatty AcidArea % C10 0.02 C12:0 0.07 C14:0 0.09 C15:0 0.05 C16:0 7.28 C16:1 0.70C17:0 0.08 C18:0 2.15 C18:1 86.32 C20:0 0.30 C20:1 0.46 C22:0 0.08 C23:00.01 C24:0 0.06

The HO and HSAO oils were methylated by known biodiesel productiontechniques to make methyl-HO and methyl-HSAO esters. These methyl esterswhere then subjection to thermal testing according to the followingprocedure:

-   -   1. Prepare equipment as shown in FIG. 1.    -   2. Add 1 litre of water to test vessel and bring to an active        boil on the hotplate.    -   3. To each test product add 50ppm Cobalt (0.083 g of 6% Cobalt        Napthenate in 100.0 gram sample) and mix thoroughly.    -   4. Weigh out, in a watch glass, 7.0 g of 100% cotton gauze, (#50        Cheese Cloth).    -   5. Evenly distribute 14.0 g of test product, as prepared in step        3, onto the gauze.    -   6. Place thermocouple (thermometer) through the center of #15        stopper. Wrap cotton around the thermocouple.    -   7. Place wrapped cotton into 24 mesh wire frame cylinder so that        it occupies the upper 4½ inches.    -   8. Position cylinder with wrapped gauze into the 1 L tall form        beaker. Secure the beaker in the boiling water and begin        recording the temperature increase with time.    -   9. Continue monitoring the temperature for 2 hours or until a 10        degree temperature drop in observed.    -   10. Plot temperature vs time on a graph.    -   11. Any sample which shows a temperature exceeding 100        degrees C. in 1 hour or 200 degrees C. in 2 hours should be        regarded as a dangerous oxidation risk or one that is likely to        spontaneously combust.

Results: The HO and HSAO methyl ester did not exhibit auto-oxidation asevidenced by a temperature rise. The control soya methyl ester sampledid exhibit the potential for auto-oxidation. The time-temperatureprofiles are shown in FIG. 18.

In addition, methylated fatty acid from oil produced by Strain Q wasfound to have the following characteristics:

-   -   Flash Point (ASTM D93) of 182° C.    -   Non-VOC    -   Kauri Butanol value (ASTM D1133) of 53.5    -   Viscosity at 40° C. (ASTM D445) of 4.57 mm2/s    -   Acid Number (ASTM D664) of 0.17 mg KOH/g    -   Boiling range distribution (ASTM D2887) 325-362° C.

Example 50 Further Properties of High Oleic (HO) andHigh-Stability-High-Oleic (HSAO) Microalgal Oils

The high oleic oil and the high-stability high-oleic algal oils can havethe properties shown in FIG. 19 or these values ±20% for the measuredparameters.

In one experiment, HSAO microalgal oil showed 512 hour stabilitymeasured by OSI at 110° C. (estimated using 130° C. data) withantioxidants of 0.5% phenyl-alpha-naphthylamine (PANA) and 500 ppmascorbyl palmitate (AP).

Example 51 Production of Low Saturate Oil by Conversion of Palmitic toPalmitoleate

As described in the examples above, genetic manipulation of microalgaecan decrease saturated fat levels, especially by increasing theproduction of oleic acid. However, in some cases, the acyl-ACPthioesterases expressed in the oleaginous cell liberate more thandesirable amounts of palmitate. Here, we describe methods for convertingpalmitate (16:0) to palmitoleate (16:1) by overexpressing apalmitoyl-ACP desaturase (PAD) gene. The PAD gene can be obtained fromnatural sources such as Macfadyena unguis (Cat's claw), Macadamiaintegrifolia (Macadamia nut), Hippophae rhamnoides (sea buckthorn), orby creating a PAD via mutation of a stearoyl-ACP desaturase to have 16:1activity. The Macfadyena unguis desaturase is denoted (MuPAD).

A high-oil-producing strain of Prototheca moriformis (Strain Z) isbiolistically transformed with plasmid DNA constructs with a PAD gene.For example, one of the high oleic strains described in the Examples 6,36, or 49 can further comprise an exogenous PAD gene. The constructscomprises sucrose invertase as a selectable marker and either the MuPADor a SAD gene (e.g., Olea europaea stearoyl-ACP desaturase, GenBankAccession No. AAB67840.1) having the L118W mutation to shiftsubstrate-specificity toward palmitate. See Cahoon, et al., PlantPhysiol (1998) 117:593-598. Both the amt3 and beta tubulin (Btub)promoters are used. In addition, the native transit peptide of a plantPAD gene can be swapped with one known to be effective in microalgae(e.g., the transit peptide from the Chlorella vularis SAD gene).

The PAD gene can be expressed in a variety of strains including thosewith a FATA knockout or knockdown and/or a KASII knockin to producehigh-oleic oil. Optionally, these strains can also producehigh-stability (low polyunsaturate) oil by virtue of a FAD (delta 12fatty acid desaturase) knockout, knockdown, or by placing FAD expressionunder control of a regulatable promoter and producing oil underconditions that downregulate FAD. In addition, useful base strains forthe introduction of PAD gene activities might also include strainspossessing KASII knockouts, and FATA Knockins, whereby levels of C16:0palmitate are elevated.

As a result, lower levels of palmitic acid are found in the fatty acidprofile of the microalgal oil as this is converted into cis-palmitoleicand cis-vaccenic acids. In some cases the total area percent ofsaturated fatty acids is less than equal to 3.5%, 3% or 2.5%.

Constructs for over expression of Macfadyena unguis C16:0 desaturase(MuPAD) follow:

1) pSZ3142: 6S::CrTUB2:ScSUC2:CvNR::PmAMT3:CpSADtp:MuPAD:CvNR::6S

Relevant Restriction Sites in the Construct pSZ31426S::CrTUB2:ScSUC2:CvNR::PmAMT3:CpSADtp:MuPAD:CvNR::6S are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA from that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene (conferring the abilityof Strain Z to metabolize sucrose) is indicated by boxed text. Theinitiator ATG and terminator TGA for invertase are indicated byuppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by an endogenous amt03promoter of Prototheca moriformis, indicated by boxed italics text. TheInitiator ATG and terminator TGA codons of the MuPAD are indicated byuppercase, bold italics, while the remainder of the coding region isindicated by bold italics. The Chlorella protothecoides S106stearoyl-ACP desaturase transit peptide is located between initiator ATGand the Asc I site. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the 6S genomic regionindicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3142:(SEQ ID NO: 99) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcctgcagagaggacagcagtgccc

gacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcga

tggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggt

agatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctc ttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

2) pSZ3145: 6S::CrTUB2:ScSUC2:CvNR::PmAMT3:MuPAD:CvNR::6S

Relevant restriction sites in the construct pSZ31456S::CrTUB2:ScSUC2:CvNR::PmAMT3: MuPAD:CvNR::6S are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Cla I, Sac I, BspQ I, respectively. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA from that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene (conferring the abilityof Strain Z to metabolize sucrose) is indicated by boxed text. Theinitiator ATG and terminator TGA for invertase are indicated byuppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by an endogenous amt03promoter of Prototheca moriformis, indicated by boxed italics text. TheInitiator ATG and terminator TGA codons of the MuPAD are indicated byuppercase, bold italics, while the remainder of the coding region isindicated by bold italics. The C. vulgaris nitrate reductase 3′ UTR isagain indicated by lowercase underlined text followed by the 6S genomicregion indicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3145: (SEQ ID NO: 100) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgacccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcctgcagagaggacagcagtgccc

gacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcga

tggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggt

cagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcaghtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagccagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

3) pSZ3137: 6S::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp:MuPAD:CvNR::6S

Relevant restriction sites in the construct pSZ31376S::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp:MuPAD:CvNR::6S are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA from that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene (conferring the abilityof Strain Z to metabolize sucrose) is indicated by boxed text. Theinitiator ATG and terminator TGA for invertase are indicated byuppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by C. reinhardtii(3-tubulin promoter, indicated by boxed italics text. The Initiator ATGand terminator TGA codons of the MuPAD are indicated by uppercase, bolditalics, while the remainder of the coding region is indicated by bolditalics. The Chlorella protothecoides S106 stearoyl-ACP desaturasetransit peptide is located between initiator ATG and the Asc I site. TheC. vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the 6S genomic region indicated by bold,lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3137:(SEQ ID NO: 101) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcctgcagagaggacagcagtgccc

gacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcga

tggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggt

agatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctc ttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Example 52 Myristate Rich Oil Produced by Overexpressing a CupheaPalustris Thioesterase

Here, we demonstrate that over expression of a Cuphea palustristhioesterase (Cpal FATB2, accession AAC49180) in UTEX1435 results in alarge increase in C14:0 production (over 60% of the fatty acid profile).

Constructs used for the overexpression of the Cpal FATB2 gene were codonoptimized for expression in P. moriformis as described herein. Cupheapalustris FATB2 is a C14 preferring thioesterase. Two constructs, bothencoding the Cpal FATB2 gene, were prepared. The first construct,pSZ2479, can be written as6SA::CrTUB2-ScSUC2-CvNR:PmAMT3-CpSAD1tpExt-CpalFATB2ExtA-CvNR::6SB. TheFatB2 coding sequence is given as SEQ ID NO: 86 and the amino acidsequence is given as SEQ ID NO: 87. The second construct, pSZ2480 can bewritten as 6SA::CrTUB2-ScSUC2-CvNR:PmAMT3-CpSAD1tpExt-CpalFATB2FLAGExtA-CvNR::6SB. The nucleic acid sequence and amino acid sequence aregiven as SEQ ID NO: 88 and SEQ ID NO: 89.

P. moriformis transformed with pSZ2480 produced high levels of myristicacid. The myristate content was 65.70 percent. This is a very largeincrease when compared to the myristate content of the wild-type oilproduced by the base strain, which has a myristate content ofapproximately 1%.

The fatty acid profile of the high myristate strain is shown in theTable 51 below.

TABLE 51 Fatty acid profile of high myristate strain. Fatty Acid % C10:00.04 C12:0 1.19 C14:0 65.7 C16:0 13.55 C18:0 0.57 C18:1 12.2 C18:2 5.13C20:0 0.05 C22:0 0.01 C24:0 0.01

Example 53 Production of Eicosenoic and Erucic Fatty Acids

In this example we demonstrate that expression of heterologous fattyacid elongase (FAE), also known as 3-ketoacyl-CoA synthase (KCS), genesfrom Cramble abyssinica (CaFAE, Accession No: AY793549), Lunaria annua(LaFAE, ACJ61777), and Cardamine graeca (CgFAE, ACJ61778) leads toproduction of very long chain monounsaturated fatty acids such aseicosenoic (20:1^(Δ11)) and erucic (22:1^(Δ13)) acids in classicallymutagenized derivative of UTEX 1435, Strain Z. On the other hand aputative FAE gene from Tropaeolum majus (TmFAE, ABD77097) and two FAEgenes from Brassica napus (BnFAE1, AAA96054 and BnFAE2, AAT65206), whileresulting in modest increase in eicosenoic (20:1^(Δ11)), produced nodetectable erucic acid in STRAIN Z. Interestingly the unsaturated fattyacid profile obtained with heterologous expression of BnFAE1 in STRAIN Zresulted in noticeable increase in Docosadienoic acid (22:2n6). All thegenes were codon optimized to reflect UTEX 1435 codon usage. Theseresults suggest that CaFAE, LaFAE or CgFAE genes encode condensingenzymes involved in the biosynthesis of very long-chain utilizingmonounsaturated and saturated acyl substrates, with specific capabilityfor improving the eicosenoic and erucic acid content.

Construct used for the expression of the Cramble abyssinica fatty acidelongase (CaFAE) in P. moriformis (UTEX 1435 strain Z)-[IpSZ3070]: Inthis example STRAIN Z strains, transformed with the construct pSZ3070,were generated, which express sucrose invertase (allowing for theirselection and growth on medium containing sucrose) and C. abyssinica FAEgene. Construct pSZ3070 introduced for expression in STRAIN Z can bewritten as 6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-CaFAE-Cvnr::6S.

The sequence of the transforming DNA is provided below. Relevantrestriction sites in the construct are indicated in lowercase, bold, andare from 5′-3′ BspQI, KpnI, XbaI, MfeI, BamHI, EcoRI, SpeI, AfIII, SacI,BspQI, respectively. BspQI sites delimit the 5′ and 3′ ends of thetransforming DNA. Bold, lowercase sequences represent genomic DNA fromSTRAIN Z that permit targeted integration at the 6S locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the C. reinhardtiiβ-tubulin promoter driving the expression of the Saccharomycescerevisiae SUC2 gene (encoding sucrose hydrolyzing activity, therebypermitting the strain to grow on sucrose) is indicated by lowercase,boxed text. The initiator ATG and terminator TGA for SUC2 are indicatedby uppercase italics, while the coding region is indicated withlowercase italics. The Chlorella vulgaris nitrate reductase (NR) gene 3′UTR is indicated by lowercase underlined text followed by an endogenousAMT3 promoter of P. moriformis, indicated by boxed italicized text. TheInitiator ATG and terminator TGA codons of the CaFAE are indicated byuppercase, bold italics, while the remainder of the gene is indicated bybold italics. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the STRAIN Z 6Sgenomic region indicated by bold, lowercase text. The final constructwas sequenced to ensure correct reading frames and targeting sequences.

Nucleotide sequence of transforming DNA contained in plasmid pSZ3070:(SEQ ID NO: 102) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgt

atgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgctcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtg

gtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttcac

ggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagcttgaagagc

Constructs used for the expression of the FAE genes from higher plantsin STRAIN Z: In addition to the CaFAE gene (pSZ3070), LaFAE (pSZ3071)from Lunaria annua, CgFAE (pSZ3072) from Cardamine graeca, TmFAE(pSZ3067) Tropaeolum majus and BnFAE1 (pSZ3068) and BnFAE2 (pSZ3069)genes from Brassica napus have been constructed for expression in STRAINZ. These constructs can be described as:

-   pSZ3071—6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-LaFAE-Cvnr::6S-   pSZ3072—6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-CgFAE-Cvnr::6S-   pSZ3067—6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-TmFAE-Cvnr::6S-   pSZ3068—6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-BnFAE1-Cvnr::6S-   pSZ3069—6S::CrTUB2-ScSUC2-Cvnr:PmAmt03-BnFAE2-Cvnr::6S

All these constructs have the same vector backbone; selectable marker,promoters, and 3′ utr as pSZ3070, differing only in the respective FAEgenes. Relevant restriction sites in these constructs are also the sameas in pSZ3070. The sequences of LaFAE, CgFAE, TmFAE, BnFAE1 and BnFAE2are shown below. Relevant restriction sites as bold text including SpeIand AfIII are shown 5′-3′ respectively.

To determine their impact on fatty acid profiles, the above constructscontaining various heterologous FAE genes, driven by the PmAMT3promoter, were transformed independently into STRAIN Z.

Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at pH7.0 (all the plasmidsrequire growth at pH 7.0 to allow for maximal FAE gene expression whendriven by the pH regulated PmAMT03 promoter). The resulting profilesfrom a set of representative clones arising from transformations withpSZ3070, pSZ3071, pSZ3072, pSZ3067, pSZ3068 and pSZ3069 into STRAIN Zare shown in Tables 52-57, respectively, below.

All the transgenic STRAIN Z strains expressing heterologous FAE genesshow an increased accumulation of C20:1 and C22:1 fatty acid (see Tables52-57). The increase in eicosenoic (20:1^(Δ11)) and erucic (22:1^(Δ13))acids levels over the wildtype is consistently higher than the wildtypelevels. Additionally, the unsaturated fatty acid profile obtained withheterologous expression of BnFAE1 in STRAIN Z resulted in noticeableincrease in Docosadienoic acid (C22:2n6). Protein alignment ofaforementioned FAE expressed in STRAIN Z is shown in FIG. 23.

TABLE 52 Unsaturated fatty acid profile in STRAIN Z and representativederivative transgenic lines transformed with pSZ3070 (CaFAE) DNA. SampleID C18:1 C18:2 C18:3a C20:1 C22:1 C22:2n6 C22:5 STRAIN Z; T588; 51.499.13 0.65 4.35 1.24 0.11 0.00 D1828-20 STRAIN Z; T588; 55.59 7.65 0.503.78 0.85 0.00 0.13 D1828-23 STRAIN Z; T588; 54.70 7.64 0.50 3.44 0.850.09 0.00 D1828-43 STRAIN Z; T588; 52.43 7.89 0.59 2.72 0.73 0.00 0.00D1828-12 STRAIN Z; T588; 56.02 7.12 0.52 3.04 0.63 0.10 0.11 D1828-19Cntrl STRAIN Z 57.99 6.62 0.56 0.19 0.00 0.06 0.05 pH7 Cntrl STRAIN Z57.70 7.08 0.54 0.11 0.00 0.05 0.05 pH5

TABLE 53 Unsaturated fatty acid profile in STRAIN Z and representativederivative transgenic lines transformed with pSZ3071 (LaFAE) DNA. SampleID C18:1 C18:2 C18:3 a C20:1 C22:1 C22:2n6 C22:5 STRAIN Z; T588; 54.667.04 0.52 1.82 0.84 0.12 0.09 D1829-36 STRAIN Z; T588; 56.27 6.72 0.511.70 0.72 0.09 0.00 D1829-24 STRAIN Z; T588; 56.65 8.36 0.54 2.04 0.670.00 0.00 D1829-11 STRAIN Z; T588; 55.57 7.71 0.53 0.10 0.66 0.00 0.00D1829-35 STRAIN Z; T588; 56.03 7.06 0.54 1.54 0.51 0.06 0.08 D1829-42Cntrl STRAIN Z 57.70 7.08 0.54 0.11 0.00 0.06 0.05 pH7 Cntrl STRAIN Z57.99 6.62 0.56 0.19 0.00 0.05 0.05 pH5

TABLE 54 Unsaturated fatty acid profile in STRAIN Z and representativederivative transgenic lines transformed with pSZ3072 (CgFAE) DNA. SampleID C18:1 C18:2 C18:3 a C20:1 C22:1 C22:2n6 C22:5 STRAIN Z; T588; 57.747.79 0.52 1.61 0.25 0.11 0.05 D1830-47 STRAIN Z; T588; 58.06 7.39 0.551.64 0.22 0.07 0.06 D1830-16 STRAIN Z; T588; 57.77 6.86 0.51 1.34 0.190.09 0.00 D1830-12 STRAIN Z; T588; 58.45 7.54 0.49 1.65 0.19 0.06 0.00D1830-37 STRAIN Z; T588; 57.10 7.28 0.56 1.43 0.19 0.07 0.00 D1830-44Cntrl STRAIN Z 57.70 7.08 0.54 0.11 0.00 0.06 0.05 pH7 Cntrl STRAIN Z57.99 6.62 0.56 0.19 0.00 0.05 0.05 pH5

TABLE 55 Unsaturated fatty acid profile in Strain AR and representativederivative transgenic lines transformed with pSZ3070 (TmFAE) DNA. Nodetectable Erucic (22:1) acid peaks were reported for these transgeniclines. Sample ID C18:1 C18:2 C18:3 a C20:1 C22:2n6 C22:5 STRAIN Z; T588;59.97 7.44 0.56 0.57 0.00 0.00 D1825-47 STRAIN Z; T588; 58.77 7.16 0.510.50 0.09 0.11 D1825-35 STRAIN Z; T588; 60.40 7.82 0.47 0.44 0.07 0.07D1825-27 STRAIN Z; T588; 58.07 7.32 0.54 0.41 0.05 0.05 D1825-14 STRAINZ; T588; 58.66 7.74 0.46 0.39 0.08 0.00 D1825-40 Cntrl STRAIN Z 57.996.62 0.56 0.19 0.05 0.05 pH7 Cntrl STRAIN Z 57.70 7.08 0.54 0.11 0.060.05 pH5

TABLE 56 Unsaturated fatty acid profile in STRAIN Z and representativederivative transgenic lines transformed with pSZ3068 (BnFAE1) DNA. Nodetectable Erucic (22:1) acid peaks were reported for these transgeniclines. Sample ID C18:1 C18:2 C18:3 a C20:1 C22:2n6 C22:5 STRAIN Z; T588;59.82 7.88 0.55 0.32 0.17 0.10 D1826-30 STRAIN Z; T588; 59.32 8.02 0.580.27 0.18 0.07 D1826-23 STRAIN Z; T588; 59.63 7.49 0.55 0.27 0.19 0.08D1826-45 STRAIN Z; T588; 59.35 7.78 0.57 0.26 0.23 0.00 D1826-24 STRAINZ; T588; 59.14 7.61 0.57 0.25 0.22 0.05 D1826-34 Cntrl STRAIN Z pH 757.81 7.15 0.59 0.19 0.04 0.06 Cntrl STRAIN Z pH 5 58.23 6.70 0.58 0.180.05 0.06

TABLE 57 Unsaturated fatty acid profile in STRAIN Z and representativederivative transgenic lines transformed with pSZ3069 (BnFAE2) DNA. Nodetectable Erucic (22:1) acid peaks were reported for these transgeniclines. Sample ID C18:1 C18:2 C18:3 a C20:1 C22:2n6 C22:5 STRAIN Z; T588;60.59 8.20 0.57 0.34 0.00 0.07 D1827-6 STRAIN Z; T588; 59.62 6.44 0.520.30 0.07 0.00 D1827-42 STRAIN Z; T588; 59.71 7.99 0.59 0.30 0.06 0.00D1827-48 STRAIN Z; T588; 60.66 8.21 0.59 0.29 0.04 0.00 D1827-43 STRAINZ; T588; 60.26 7.99 0.57 0.28 0.04 0.00 D1827-3 Cntrl STRAIN Z pH 757.81 7.15 0.59 0.19 0.04 0.06 Cntrl STRAIN Z pH 5 58.23 6.70 0.58 0.180.05 0.06

Example 54 Elevating Total Unsaturated Fatty Acids Level by ExpressingHeterologous Desaturase Genes

One of the approaches to generate a “zero SAT FAT” (e.g., totalunsaturated fatty acids target at 97% or more/less than or equal to 3%saturated fat) strain is to express desaturase genes in a high oleicstrain such as Strain N, which we found to produce about 85% C18:1 withtotal un-saturates around 93% in multiple fermentation runs. Weinvestigated if the total saturates will be further diminished byexpressing desaturase genes in Strain N.

In the examples below, we demonstrated the ability to reduce stearic andpalmitic levels in wild type strain UTEX1435 by over expression ofheterologous stearoyl-ACP desaturase genes, including desaturases fromOlea europaea, Ricinus communis, and Chlorella protothecoides.

Construct used for the expression of the Olea europaea stearoyl-ACPdesaturase: To introduce the O. europaea stearoyl-ACP desaturase(Accession No: AAB67840.1) into UTEX1435, Strain A, the Saccharomycescerevisiae invertase gene was utilized as the selectable marker toconfer the ability of growing on sucrose media. The construct that hasbeen expressed in UTEX1435, Strain A can be written as6SA::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp:OeSAD:CvNR::65B and is termedpSZ1377.

Relevant restriction sites in the construct pSZ1377 are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene is indicated by boxedtext. The initiator ATG and terminator TGA for invertase are indicatedby uppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the second C.reinhardtii β-tubulin promoter driving the expression of the OeSAD,indicated by boxed italics text. The Initiator ATG and terminator TGAcodons of the OeSAD are indicated by uppercase, bold italics, while theremainder of the stearoyl-ACP desaturase coding region is indicated bybold italics. The Chlorella protothecoides stearoyl-ACP desaturasetransit peptide is located between initiator ATG and the Asc I site. TheC. vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the 6S genomic region indicated by bold,lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ 1377:(SEQ ID NO: 108) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcgg

ccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtg

agtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtc

gctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctc ttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctaccccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagcttgaagagc

Construct used for the expression of the Ricinus communis stearoyl-ACPdesaturase: To introduce the Ricinus communis stearoyl-ACP desaturase(Accession No: AAA74692.1) into UTEX1435, Strain A, the Saccharomycescerevisiae invertase gene was utilized as the selectable marker toconfer the ability of growing on sucrose media. The construct that hasbeen expressed in UTEX1435, Strain A can be written as6SA::CrTUB2:ScSUC2:CvNR::PmAMT03:CpSADtp:RcSAD:CvNR::6SB and is termedpSZ1454.

Relevant restriction sites in the construct pSZ1454 are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA that permit targetedintegration at 6s nuclear chromosomal locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the C. reinhardtiiβ-tubulin promoter driving the expression of the yeast sucrose invertasegene is indicated by boxed text. The initiator ATG and terminator TGAfor invertase are indicated by uppercase, bold italics while the codingregion is indicated in lowercase italics. The Chlorella vulgaris nitratereductase 3′ UTR is indicated by lowercase underlined text followed bythe endogenous AMT03 promoter driving the expression of the RcSAD,indicated by boxed italics text. The Initiator ATG and terminator TGAcodons of the RcSAD are indicated by uppercase, bold italics, while theremainder of the stearoyl-ACP desaturase coding region is indicated bybold italics. The Chlorella protothecoides stearoyl-ACP desaturasetransit peptide is located between initiator ATG and the Asc I site. TheC. vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the 6S genomic region indicated by bold,lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ1454:(SEQ ID NO: 109) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcc

cgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgac

ggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatg

actgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagct cttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagcttgaagagc

Construct used for the expression of the Chlorella protothecoidesstearoyl-ACP desaturase: To introduce the Chlorella protothecoidesstearoyl-ACP desaturase into UTEX1435, Strain Z, the Saccharomycescerevisiae invertase gene was utilized as the selectable marker toconfer the ability of growing on sucrose media. The construct that hasbeen expressed in UTEX1435, Strain Z can be written as6SA::CrTUB2:ScSUC2:CvNR::PmAMT03:CpSAD1:CvNR::6SB and is termed pSZ3144.

Relevant restriction sites in the construct pSZ3144 are indicated inlowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, Xba I, MfeI, BamH I, EcoR I, Spe I, Cla I, Sac I, BspQ I, respectively. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA that permit targetedintegration at 6s locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii -tubulin promoter driving theexpression of the yeast sucrose invertase gene is indicated by boxedtext. The initiator ATG and terminator TGA for invertase are indicatedby uppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the endogenous AMT03promoter driving the expression of the CpSAD1, indicated by boxeditalics text. The Initiator ATG and terminator TGA codons of the CpSAD1are indicated by uppercase, bold italics, while the remainder of thestearoyl-ACP desaturase coding region is indicated by bold italics. TheC. vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the 6S genomic region indicated by bold,lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3144:(SEQ ID NO: 110) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcctgcagagaggacagcagtgccc

gacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgcccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcga

tggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggt

ccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagag ctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at either pH5.0 or pH7.0,depending on the promoters that drive the expression of the desaturasegenes. Transgenic lines arising from the transformations with pSZ1377(D583) were assayed in (low-nitrogen) lipid production media at pH5.0,because of the nature of the promoters and the fact that P. moriformisproduces more lipid at pH5.0. Transgenic lines generated from thetransformation of pSZ1454 (D648) and pSZ3144 (D1923) are assayed at pH7.0 to allow for maximal desaturase gene expression when driven by thepH regulated PmAMT3 promoter. The resulting profiles from representativeclones arising from transformations with D583, D648, and D1923 are shownin Tables 58, 59 and 60, respectively, below. The result of expressionof OeSAD and CpSAD1 genes is a clear diminution of C18:0 chain lengthswith an increase in C18:1. Also we noticed that there is a subtleincrease in the level of C16:1, indicating these stearoyl-ACPdesaturases may have broad specificity. The transformants resulted fromthe expression of RcSAD gene also diminishes in the level of C18:0, andelevation in C16:1. Notably, C16:1 could be increased from under 1% toover 1.5% or over 2%. However, there is also a drop in the level ofC18:1 fatty acid and increase in C18:2, which may be caused by thegrowth defect of these transgenic lines.

TABLE 58 Lipid profile of representative clones arising fromtransformation with D583 (pSZ1377) DNA Sample ID C16:0 C16:1 C18:0 C18:1C18:2 D583-25 19.20 1.53 1.15 64.08 11.76 D583-10 21.86 0.99 1.77 61.4311.42 D583-3 21.94 0.95 1.85 62.22 10.53 D583-33 20.76 0.95 1.85 61.7612.17 D583-26 20.18 0.92 1.89 62.56 11.97 D583-1 21.28 0.95 1.90 62.6310.94 S1331 25.48 0.71 3.23 59.70 8.25

TABLE 59 Lipid profile of representative clones arising fromtransformation with D648 (pSZ1454) DNA Sample ID C16:0 C16:1 C18:0 C18:1C18:2 D648-9 26.92 2.30 1.12 54.27 11.30 D648-28 26.54 2.50 1.32 52.5812.90 D648-15 29.47 1.68 1.48 51.74 11.48 D648-12 27.39 1.41 1.66 54.4511.58 D648-43 29.74 1.52 1.68 52.59 10.85 D648-7 26.98 1.62 1.69 54.5111.39 S1331-pH 7 25.86 0.96 2.84 58.33 9.16

TABLE 60 Lipid profile of representative clones arising fromtransformation with D1923 (pSZ3144) DNA. Sample ID C14:0 C14.1 C16:0C16:1 C18:0 C18:1 C18:2 Block 2; E2; pH7; 1.46 0.11 20.74 2.54 0.8663.99 9.03 STRAIN Z; T613; D1923-2 Block 2; G12; pH7; 1.52 0.10 25.201.97 1.67 61.10 7.38 STRAIN Z; T613; D1923-36 Block 2; E8; pH7; 1.480.09 26.41 1.78 1.54 60.54 7.01 STRAIN Z; T613; D1923-8 Block 2; F3;1.50 0.07 25.87 1.75 1.62 61.25 6.94 pH7STRAIN Z; T613; D1923-15 Block2; F9; pH7; 1.47 0.07 27.02 1.73 1.84 60.15 6.55 STRAIN Z; T613;D1923-21 Block 2; F4; pH7; 1.44 0.07 24.30 1.71 1.41 62.79 7.29 STRAINZ; T613; D1923-16 pH7 STRAIN Z 1.47 0.00 28.25 0.82 3.16 58.27 6.72

Example 55 Generation of Palmitoleic Acid by Introducing Mutated (L118W)Stearoyl-ACP Desaturases

To generate lower total saturates (Zero SAT FAT) strains, we haveintroduced both putative stearoyl-ACP desaturases (SAD) andpalmitoyl-ACP desaturase (PAD) genes into Prototheca moriformis. Wefound that a single amino acid substitution (L118W) in P. moriformisSAD2-1 and Olea europaea SAD resulted in an increase in desaturation ofpalmitate moieties in the triglycerides produced by the cell. Oils withfatty acid profiles of over 5% palmitoleic acid were produced in theresulting transgenic lines. Therefore, these mutated SADs could be veryuseful to elevate palmitoleic as a route to lower total saturates, or toobtain palmitoleic acid containing oils. Oils with over 2, 3, 4, and 5area% palmitoleic were obtained.

The Saccharomyces cerevisiae invertase gene (Accession no: NP 012104)was utilized as the selectable marker to introduce the Protothecamoriformis stearoyl-ACP desaturase PmSAD2-1 (L118W) and Olea europaeastearoyl-ACP desaturase OeSAD (L118W) into 6S nuclear chromosomal locusof P. moriformis strain Z by homologous recombination using previouslydescribed biolistic transformation methods.

The constructs that have we used to transform Strain Z can be writtenas:

-   1)6SA::CrTUB2:ScSUC2:CvNR::PmUAPA1: PmSAD2-1(L118W)-CvNR::6SB    (pSZ3305, D2066)-   2) 6SA::CrTUB2:ScSUC2:CvNR::CrTUB2: PmSAD2-1(L118W)-CvNR::6SB    (pSZ3299, D2060)-   3) 6SA::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp-OeSAD (L118W)-CvNR::6SB    (pSZ3298, D2059)

Construct pSZ3305: 6SA::CrTUB2:ScSUC2:CvNR::PmUAPA1:PmSAD2-1(L118W)-CvNR::6SB The sequence of the pSZ3305 transforming DNAis provided below. Relevant restriction sites in pSZ33056SA::CrTUB2:ScSUC2:CvNR::PmUAPA1: PmSAD2-1(L118W)-CvNR::6SB areindicated in lowercase, bold and underlining and are 5′-3′ BspQ 1, KpnI, Asc I, Mfe I, EcoRV, SpeI, AscI, ClaI, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent 6SA genomic DNA that permit targetedintegration at 6S locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene is indicated by boxedtext. The initiator ATG and terminator TGA for invertase are indicatedby uppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the P. moriformisUAPA1 promoter, indicated by boxed italics text. The initiator ATG andterminator TGA codons of the PmSAD2-1 (L118W) are indicated byuppercase, bold italics, while the remainder of the coding region isindicated by bold italics. The C. vulgaris nitrate reductase 3′ UTR isagain indicated by lowercase underlined text followed by the 6SB genomicregion indicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3305:(SEQ ID NO: 111) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctcggcc

cctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgaca

gactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatg

tcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Construct pSZ3299: 6SA::CrTUB2:ScSUC2:CvNR::CrTUB2:PmSAD2-1(L118W)-CvNR::6SB The sequence of the pSZ3299 transforming DNAis provided in Sequence 56-2. Relevant restriction sites in pSZ32996SA::CrTUB2:ScSUC2:CvNR::CrTUB2:PmSAD2-1(L118W)-CvNR::65B are indicatedin lowercase, bold and underlining and are 5′-3′ BspQ 1, Kpn I, XbaI,Mfe I, EcoRV, SpeI, AscI, ClaI, Sac I, BspQ I, respectively. BspQI sitesdelimit the 5′ and 3′ ends of the transforming DNA. Bold, lowercasesequences represent 6SA genomic DNA that permit targeted integration at6S locus via homologous recombination. Proceeding in the 5′ to 3′direction, the C. reinhardtii β-tubulin promoter driving the expressionof the yeast sucrose invertase gene is indicated by boxed text. Theinitiator ATG and terminator TGA for invertase are indicated byuppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the C. reinhardtiiβ-tubulin promoter, indicated by boxed italics text. The Initiator ATGand terminator TGA codons of the PmSAD2-1 (L118W) are indicated byuppercase, bold italics, while the remainder of the coding region isindicated by bold italics. The C. vulgaris nitrate reductase 3′ UTR isagain indicated by lowercase underlined text followed by the 6SB genomicregion indicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3299:(SEQ ID NO: 112) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctc

ggccggcttcgccgccaagatcagcgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGA caattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggt

cgtggccgctcctggccgacgcgctgcctctcgtcctctggtggtgcacgccgtggcctccgaggctcctctgggcgtgcctccctccgtgcagcgcccttctcccgtggtgtactccaagctggacaagcagcaccgcctgacgcctgagcgcctggagctggtgcagtccatgggccagttcgccgaggagcgcgtgctgcccgtgctgcaccccgtggacaagctgtggcagccccaggacttcctgcccgaccccgagtcccccgacttcgaggaccaggtggccgagctgcgcgcccgcgccaaggacctgcccgacgagtacttcgtggtgctggtgggcgacatgatcaccgaggaggccctgcccacctacatggccatgctgaacacctgggacggcgtgcgcgacgacaccggcgccgccgaccacccctgggcccgctggacccgccagtgggtggccgaggagaaccgccacggcgacctgctgaacaagtactgctggctgaccggccgcgtgaacatgcgcgccgtggaggtgaccatcaacaacctgatcaagtccggcatgaacccccagaccgacaacaacccctacctgggcttcgtgtacacctccttccaggagcgcgccaccaagtactcccacggcaacaccgcccgcctggccgccgagcacggcgacaagggcctgtccaagatctgcggcctgatcgcctccgacgagggccgccacgagatcgcctacacccgcatcgtggacgagttcttccgcctggaccccgagggcgccgtggccgcctacgccaacatgatgcgcaagcagatcaccatgcccgcccacctgatggacgacatgggccacggcgaggccaaccccggccgcaacctgttcgccgacttctccgccgtggccgagaagatcgacgtgtacgacgccgaggactactgccgcatcctggagcacctgaacgcccgctggaaggtggacgagcgccaggtgtccggccaggccgccgccgaccaggagtacgtgctgggcctgccccagcgcttccgcaagctggccgagaagaccgccgccaagcgcaagcgcgtggcccgccgccccgtggccttctcctggatctccggccgcgagatcatggtgTGAatc gatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Construct pSZ3298:6SA::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp-OeSAD(L118W)-CvNR::6SB Thesequence of the pSZ3299 transforming DNA is provided below. Relevantrestriction sites in the construct pSZ32986SA::CrTUB2:ScSUC2:CvNR::CrTUB2:CpSADtp-OeSAD(L118W)-CvNR::6SB areindicated in lowercase, bold and underlining and are 5′-3′ BspQ 1, KpnI, XbaI, Mfe I, EcoRV, SpeI, AscI, ClaI, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent 6SA genomic DNA that permit targetedintegration at 6S locus via homologous recombination. Proceeding in the5′ to 3′ direction, the C. reinhardtii β-tubulin promoter driving theexpression of the yeast sucrose invertase gene is indicated by boxedtext. The initiator ATG and terminator TGA for invertase are indicatedby uppercase, bold italics while the coding region is indicated inlowercase italics. The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the C. reinhardtiiβ-tubulin promoter, indicated by boxed italics text. The Initiator ATGand terminator TGA codons of the OeSAD (L118W) are indicated byuppercase, bold italics, while the remainder of the coding region isindicated by bold italics. The Chlorella protothecoides S106stearoyl-ACP desaturase transit peptide is located between initiator ATGand the Asc I site. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the 6SB genomicregion indicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3298:(SEQ ID NO: 113) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctc

ggccggcttcgccgccaagatcagcgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGA caattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaa

tcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcg ggcgcgccgaggtgcacgtgcaggtgacccactccctggcccccgagaagcgcgagatcttcaactccctgaacaactgggcccaggagaacatcctggtgctgctgaaggacgtggacaagtgctggcagccctccgacttcctgcccgactccgcctccgagggcttcgacgagcaggtgatggagctgcgcaagcgctgcaaggagatccccgacgactacttcatcgtgctggtgggcgacatgatcaccgaggaggccctgcccacctaccagaccatgctgaacacctgggacggcgtgcgcgacgagaccggcgcctccctgaccccctgggccatctggacccgcgcctggaccgccgaggagaaccgccacggcgacctgctgaacaagtacctgtacctgtccggccgcgtggacatgaagcagatcgagaagaccatccagtacctgatcggctccggcatggacccccgcaccgagaacaacccctacctgggcttcatctacacctccttccaggagcgcgccaccttcatctcccacggcaacaccgcccgcctggccaaggagcacggcgacctgaagctggcccagatctgcggcatcatcgccgccgacgagaagcgccacgagaccgcctacaccaagatcgtggagaagctgttcgagatcgaccccgacggcaccgtgctggccctggccgacatgatgcgcaagaaggtgtccatgcccgcccacctgatgtacgacggccaggacgacaacctgttcgagaacttctcctccgtggcccagcgcctgggcgtgtacaccgccaaggactacgccgacatcctggagttcctggtgggccgctgggacatcgagaagctgaccggcctgtccggcgagggccgcaaggcccaggactacgtgtgcaccctgcccccccgcatccgccgcctggaggagcgcgcccagtcccgcgtgaagaaggcctccgccacccccttctcctggatcttcggccgcgagatcaacctgatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGAatcgatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at pH5.0. The resultingprofiles from representative clones arising from transformations withpSZ3305, pSZ3299 and pSZ3298 into Strain Z are shown in Tables 61-63respectively. Thus, introductions of such mutations or genes canincrease levels of palmitoleic acid and decrease levels of saturation inthe fatty acid profiles of oils produced by recombinant microalgae. Oilswere obtained with C16:1/C16:0 ratios of at least 0.1, 0.15, and 0.18.

TABLE 61 Fatty acid profiles in Strain Z and derivative transgenic linestransformed with pSZ3305 (D2066). C16:1: C16:0 Sample ID C14:0 C16:0C16:1 C18:0 C18:1 C18:2 ratio pH5; T657; 1.27 24.73 4.55 3.63 58.62 5.840.18 D2066-29 pH5; T657; 1.27 22.89 3.94 3.17 60.69 6.61 0.17 D2066-16pH5; T657; 1.33 25.47 3.07 3.58 59.32 5.86 0.12 D2066-36 pH5; T657; 1.2822.48 2.42 3.66 61.65 7.02 0.11 D2066-19 pH5;; T657; 1.29 26.25 2.263.99 59.27 5.50 0.09 D2066-12 pH5; T657; 1.33 24.49 2.26 3.24 61.42 6.010.09 D2066-21 pH5; Strain Z 1.40 27.70 0.89 3.91 57.34 7.05 0.03 (200:1)

TABLE 62 Fatty acid profiles in Strain Z and derivative transgenic linestransformed with pSZ3299 (D2060). C16:1: C16:0 Sample ID C14:0 C16:0C16:1 C18:0 C18:1 C18:2 ratio pH5; T655; D2060-9 1.35 24.67 2.73 3.2160.34 6.22 0.11 pH5; T655; D2060-23 1.52 30.05 2.64 1.65 55.38 7.03 0.09pH5; T655; D2060-21 1.29 23.54 2.43 2.94 62.25 6.18 0.10 pH5; T655;D2060-2 1.29 24.30 2.22 2.57 62.09 6.28 0.09 pH5; T655; D2060-12 1.3727.67 1.90 2.84 59.69 5.41 0.07 pH5; T655; D2060-14 1.41 25.01 1.62 2.4761.30 6.96 0.06 pH5 Strain Z 1.40 27.89 0.87 3.25 57.84 7.19 0.03

TABLE 63 Fatty acid profiles in Strain Z and derivative transgenic linestransformed with pSZ3298 (D2059). C16:1: C16:0 Sample ID C14:0 C16:0C16:1 C18:0 C18:1 C18:2 ratio pH5; T655; D2059-21 1.09 25.44 5.04 1.8654.78 10.44 0.19 pH5; T655; D2059-19 1.28 23.11 2.71 2.19 60.66  8.640.12 pH5; T655; D2059-4 1.68 28.19 1.61 2.54 58.39  6.37 0.06 pH5; T655;D2059-23 1.37 23.25 1.45 2.92 62.15  7.44 0.06 pH5; T655; D2059-1 1.3823.34 1.28 2.68 62.31  7.62 0.05 pH5 Strain Z 1.40 27.89 0.87 3.25 57.84 7.19 0.03

Example 56 Down Regulation of FATA and Over Expression of the ProtothecaMoriformis KETO-Acyl-ACP Synthase II (PMKASII) Gene

A transgenic P. moriformis line was created with downregulation of anendogenous FATA1 gene combined with overexpression of an endogenousKASII gene. The resulting strain produced a triglyceride-rich oil thatwas enriched in oleate.

In the example below, we have followed up on previous work demonstratingthat triacylglycerols in algae can be significantly enriched in levelsof oleate (C18:1) utilizing molecular genetic approaches, such as downregulating endogenous FATA1 (a single FATA allele) and over-expressionof endogenous KASII activity. In this example, we focus our efforts oncombining these approaches into a single transgenic line. Constructsthat disrupt a single copy of the FATA1 allele while simultaneouslyoverexpressing the P. moriformis KASII gene (PmKASII). were introducedinto a high oleic Prototheca moriformis Strain AO. Strain AO was derivedfrom a high 18:1 producing mutant derived from UTEX 1435 using classicalmutagenesis techniques. One of the resulting strains, termed Strain AP,produced an oil with a fatty acid profile having 85% C18:1 with totalun-saturates around 93% in multiple fermentation runs. The strain APalso had high lipid productivity.

The Saccharomyces cerevisiae invertase gene (Accession no: NP 012104)was utilized as the selectable marker to introduce the PmKASII into theFATA1 nuclear chromosomal locus of P. moriformis strain AO by homologousrecombination using biolistic transformation. To investigate the KASIIactivity when driven by different promoters, PmKASII was fused toseveral promoters: PmUAPA1, PmLDH1, and PmAMT3. Note that theintegration constructs are all designed as reverse orientation to theFATA1 gene; this was found to give a greater likelihood of stableinvertase expression. Therefore, the constructs that have been expressedin Strain AH can be written as:

-   1)FATA1 3′::CrTUB2:ScSUC2:CvNR::PmUAPA1:PmKASII-CvNR::FATA1 5′    (pSZ2533)-   2) FATA1 3′::CrTUB2:ScSUC2:CvNR::PmLDH1:PmKASII-CvNR::FATA1 5′    (pSZ2532)-   3) FATA1 3′::CrTUB2:ScSUC2:CvNR::PmAMT3:PmKASII-CvNR::FATA1 5′    (pSZ2750)

Strain AP is one of the transformants generated from pSZ2533. Relevantrestriction sites in the construct pSZ2533FATA13′::CrTUB2:ScSUC2:CvNR::PmUAPA1:PmKASII-CvNR::FATA1 5′ areindicated in lowercase, bold and underlining and are 5′-3′ BspQ 1, KpnI, Asc I, Mfe I, EcoRV, SpeI, AscI, ClaI, Sac I, BspQ I, respectively.BspQI sites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent FATA1 3′ genomic DNA that permit targetedintegration at FATA1 locus via homologous recombination. Proceeding inthe 5′ to 3′ direction, the C. reinhardtii β-tubulin promoter drivingthe expression of the yeast sucrose invertase gene is indicated by boxedtext. The initiator ATG and terminator TGA for invertase are indicatedby uppercase, bold italics while the coding region is indicated inlowercase italics The Chlorella vulgaris nitrate reductase 3′ UTR isindicated by lowercase underlined text followed by the P. moriformisUAPA1 promoter, indicated by boxed italics text. The Initiator ATG andterminator TGA codons of the PmKASII are indicated by uppercase, bolditalics, while the remainder of the coding region is indicated by bolditalics. The Chlorella protothecoides S106 stearoyl-ACP desaturasetransit peptide is located between initiator ATG and the Asc I site. TheC. vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the FATA1 5′ genomic region indicated bybold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ2533:(SEQ ID NO: 114) gctcttcacccaactcagataataccaatacccctccttctcctcctcatccattcagtacccccccccttctcttcccaaagcagcaagcgcgtggcttacagaagaacaatcggcttccgccaaagtcgccgagcactgcccgacggcggcgcgcccagcagcccgcttggccacacaggcaacgaatacattcaatagggggcctcgcagaatggaaggagcggtaaagggtacaggagcactgcgcacaaggggcctgtgcaggagtgactgactgggcgggcagacggcgcaccgcgggcgcaggcaagcagggaagattgaagcggcagggaggaggatgctgattgaggggggcatcgcagtctctcttggacccgggataaggaagcaaatattcggccggttgggttgtgtgtgtgcacgttttcttcttcagagtcgtgggtgtgcttccagggaggatataagcagcaggatcgaatcccgcgacca

catgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaag TGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttcacagccta

gggctccgggccccggcgcccagcgaggcccctccccgtgcgcg ggcgcgccgccgccgccgccgacgccaaccccgcccgccccgagcgccgcgtggtgatcaccggccagggcgtggtgacctccctgggccagaccatcgagcagttctactcctccctgctggagggcgtgtccggcatctcccagatccagaagttcgacaccaccggctacaccaccaccatcgccggcgagatcaagtccctgcagctggacccctacgtgcccaagcgctgggccaagcgcgtggacgacgtgatcaagtacgtgtacatcgccggcaagcaggccctggagtccgccggcctgcccatcgaggccgccggcctggccggcgccggcctggaccccgccctgtgcggcgtgctgatcggcaccgccatggccggcatgacctccttcgccgccggcgtggaggccctgacccgcggcggcgtgcgcaagatgaaccccttctgcatccccttctccatctccaacatgggcggcgccatgctggccatggacatcggcttcatgggccccaactactccatctccaccgcctgcgccaccggcaactactgcatcctgggcgccgccgaccacatccgccgcggcgacgccaacgtgatgctggccggcggcgccgacgccgccatcatcccctccggcatcggcggcttcatcgcctgcaaggccctgtccaagcgcaacgacgagcccgagcgcgcctcccgcccctgggacgccgaccgcgacggcttcgtgatgggcgagggcgccggcgtgctggtgctggaggagctggagcacgccaagcgccgcggcgccaccatcctggccgagctggtgggcggcgccgccacctccgacgcccaccacatgaccgagcccgacccccagggccgcggcgtgcgcctgtgcctggagcgcgccctggagcgcgcccgcctggcccccgagcgcgtgggctacgtgaacgcccacggcacctccacccccgccggcgacgtggccgagtaccgcgccatccgcgccgtgatcccccaggactccctgcgcatcaactccaccaagtccatgatcggccacctgctgggcggcgccggcgccgtggaggccgtggccgccatccaggccctgcgcaccggctggctgcaccccaacctgaacctggagaaccccgcccccggcgtggaccccgtggtgctggtgggcccccgcaaggagcgcgccgaggacctggacgtggtgctgtccaactccttcggcttcggcggccacaactcctgcgtgatcttccgcaagtacgacgagatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGA atcgatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaaccgaatgctgcgtgaacgggaaggaggaggagaaagagtgagcagggagggattcgtgtcctctgatcatcatgcgattgattacgttgaatgcgacggccggtcagccccggacctccacgcaccgcagaaatgagaaatgagaggtgaaggaacgcatccctatgcccttgcaatggacagtgtttctggccaccgccaccaagacttgtgctcctccaggaagatgcgcttgtcctccgccatcttgcagggctcaagctgctcccaaaactcttgggcgggttccggacggacggctaccgcgggtgcggccctgaccgccactgttcggaagcagcggcgctgcatgggcagcggccgctgcggtgcgccacggaccgcatgatccaccggaaaagcgcacgcgctggagcgcgcagaggaccacagagaagcggaagagacgccagtactggcaagcaggctggtcggtgccatggcgcgctactaccctcgctatgactcgggtcctcggccggctggcggtgctgacaattcgtttagtggagcagcgactccattcagctaccagtcgaactcagtggcacagtgactccgctcttc

In addition to the construct pSZ2533, we also investigated the PmKASIIactivity when the KASII gene driven by other promoters, includingPmLDH1, and PmAMT3. The plasmid pSZ2532 can be written as FATA13′::CrTUB2:ScSUC2:CvNR::PmLDH1:PmKASII-CvNR::FATA1 5′, while the plasmidpSZ2750 can be written as FATA1 3′::CrTUB2:ScSUC2:CvNR::PmAMT3:PmKASII-CvNR::FATA1 5′. Since the sequences of these twoplasmids are the same as pSZ2533 except for the promoter that drives thePmKASII, the following sequences only show the sequence of the PmLDH1and PmAMT3 promoters.

Nucleotide sequence of PmLDH1 promoter that drive the expression of PmKASII in pSZ2532:(SEQ ID NO: 115)

Nucleotide sequence of PmAMT3 promoter that drive the expression of PmKASII in pSZ2750:(SEQ ID NO: 116)

Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at either pH5.0 or pH7.0,depend on the promoters that driven the expression of the PmKASII gene.Transgenic lines arising from the transformations with pSZ2533 (D1636)and pSZ2532 (D1637) were assayed in lipid production media at pH5.0,because of the nature of the promoters and the fact that P. moriformisproduces more lipid at pH5.0. Transgenic lines generated from thetransformation of pSZ2750 (D1684) were assayed at pH 7.0 to allow formaximal PmKASII gene expression when driven by the pH regulated PmAMT3promoter. The resulting profiles from representative clones arising fromtransformations with D1636 (pSZ2533), D1637 (pSZ2532), and D1684(pSZ2750) are shown in Tables 64-66, respectively.

The impact of FATA1 knock-out and simultaneously overexpressing the P.moriformis KASII gene is a clear diminution of C16:0 chain lengths witha significant increase in C18:1. At pH5.0, it appears that PmUAPA1 isstronger than PmLDH1, the palmitate level in D1636 transformants isclose to 3%, while none of the transformants in D1637 go below 7% at thesame condition.

TABLE 64 Lipid profile of representative clones arising fromtransformation with D1636 (pSZ2533) DNA. Sample ID C14:0 C16:0 C18:0C18:1 C18:2 pH 5; T523; D1636-3 0.53 3.31 6.15 79.89 7.19 pH 5; T523;D1636-4 0.48 3.54 5.34 80.78 6.92 pH 5; T523; D1636-5 0.48 3.59 5.4181.37 6.55 pH 5; T523; D1636-12 0.61 3.59 3.67 80.52 8.93 pH 5; T523;D1636-13 0.55 3.80 4.88 81.83 6.61 pH 5; T523; D1636-21 0.54 4.18 2.8282.26 8.17 pH 5; Strain AO 0.89 17.28 2.69 70.53 6.86

TABLE 65 Lipid profile of representative clones arising fromtransformation with D1637 (pSZ2532) DNA. Sample ID C14:0 C16:0 C18:0C18:1 C18:2 pH 5; T523; D1637-6 0.46 7.64 3.43 80.08 6.33 pH 5; T523;D1637-12 0.66 8.49 1.90 77.06 9.59 pH 5; T523; D1637-13 0.47 8.59 3.1879.39 6.54 pH 5; T523; D1637-15 0.60 9.60 2.51 76.41 8.85 pH 5; T523;D1637-7 0.61 11.16 2.21 75.82 8.04 pH 5; T523; D1637-8 0.93 11.29 3.6174.84 6.61 pH 5; Strain AO 0.89 17.28 2.69 70.53 6.86

TABLE 66 Lipid profile of representative clones arising fromtransformation with D1684 (pSZ2750) DNA. Sample ID C14:0 C16:0 C18:0C18:1 C18:2 pH 7; T532; D1684-14 0.55 5.04 4.90 78.88 8.19 pH 7; T532;D1684-23 0.58 5.80 4.98 77.51 8.69 pH 7; T532; D1684-1 0.59 6.37 4.9977.47 8.03 pH 7; T532; D1684-24 0.55 6.37 4.83 77.98 7.73 pH 7; T532;D1684-11 0.61 6.61 4.88 76.14 8.96 pH 7; T532; D1684-16 0.57 6.61 5.0177.74 7.83 pH 7; Strain AO 0.84 20.12 3.52 66.86 6.77

Example 57 Generation of a High-Oleic High-Stability (HOHS)Oil-Producing Strain

Strain AP of Example 56 produces oil with about 85% oleic acid withtotal un-saturates around 93%. Here we show that that that the oxidativestability of the high-oleic oil can be improved by knock-down of a delta12 fatty acid desaturase, thereby reducing linoleic acid production inthe oleaginous cell.

We expressed a hairpin-RNA-producing construct in Strain AP targeting anendogenous FAD gene, PmFAD2. The resulting strains, including Strain AQ,produce >90% C18:1 and <1% C18:2 in fermenters. Most importantly, StrainAQ retains the same level of lipid productivity and sucrose hydrolyzingability as its parental strain, Strain AP.

Generation of high oleic high stability oil producing strain AQ:Construct used for down regulating PmFAD2. To generate a strain thatproduces oil with high oxidative stability, the hairpin PmFAD2 wasintroduced into AP for down regulating PmFAD2 expression. Strain AQ is astable line generated from the transformation of pSZ3372 DNA(6SA::PmHXT1:ScarMEL1:CvNR::CrTUB2: Hairpin PmFAD2:CvNR::6SB) intoStrain AP. In this construct, the Saccharomyces carlbergensis MEL1 genewas utilized as the selectable marker to introduce the Hairpin PmFAD2into the 6S nuclear chromosomal locus of P. moriformis strain AQ byhomologous recombination using previously described transformationmethods (biolistics).

The sequence of the pSZ3372 transforming DNA is provided below. Relevantrestriction sites in pSZ3372 are indicated in lowercase, bold andunderlining and are 5′-3′ BspQ 1, Kpn I, SpeI, Mfe I, BamHI, EcoRV,SpeI, XhoI, SacI, BspQ I, respectively. BspQI sites delimit the 5′ and3′ ends of the transforming DNA. Bold, lowercase sequences represent 6SAgenomic DNA that permits targeted integration at 6S locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the P. moriformisHXT1 promoter driving the expression of the S. carlbergensis MEL1 geneis indicated by boxed text. The initiator ATG and terminator TGA forScarMEL1 are indicated by uppercase, bold italics while the codingregion is indicated in lowercase italics. The Chlorella vulgaris nitratereductase 3′ UTR is indicated by lowercase underlined text followed bythe C. reinhardtii β-tubulin promoter, indicated by boxed italics text.The hairpin PmFAD2 cassette includes the P. moriformis FAD2 exon1(indicated by italics underlined text), the intron of PmFAD2 (italicslowercase text), and followed by the inverted PmFAD2 exon1 (indicated byitalics underlined text). The C. vulgaris nitrate reductase 3′ UTR isagain indicated by lowercase underlined text followed by the 6SB genomicregion indicated by bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ3372:(SEQ ID NO: 117) gctcttcgccgccgccactcctgctcgagcgcgcccgcgcgtgcgccgccagcgccttggccttttcgccgcgctcgtgcgcgtcgctgatgtccatcaccaggtccatgaggtctgccttgcgccggctgagccactgcttcgtccgggcggccaagaggagcatgagggaggactcctggtccagggtcctgacgtggtcgcggctctgggagcgggccagcatcatctggctctgccgcaccgaggccgcctccaactggtcctccagcagccgcagtcgccgccgaccctggcagaggaagacaggtgaggggggtatgaattgtacagaacaaccacgagccttgtctaggcagaatccctaccagtcatggctttacctggatgacggcctgcgaacagctgtccagcgaccctcgctgccgccgcttctcccgcacgcttctttccagcaccgtgatggcgcgagccagcgccgcacgctggcgctgcgcttcgccgatctgaggacagtcggggaactctgatcagtctaaacccccttgcgcgttagtgttgccatcctttgcagaccggtgagagccgacttgttgtgcgccaccccccacaccacctcctcccagaccaattctgtcacctttttggcgaaggcatcggcctc

ccctgaagggcgtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctcc TGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaaacgttc

cactgtttcgagcgctcggcgcttcgtagcagcatgtacctggcctttgacatcgcggtcatgtccctgctctacgtcgcgtcgacgtacatcgaccctgcaccggtgcctacgtgggtcaagtacggcatcatgtggccgctctactggttcttccaggtgtgtttgagggttttggttgcccgtattgaggtcctggtggcgcgcatggaggagaaggcgcctgtcccgctgacccccccggctaccctcccggcaccttccagggcgcgtacgggaagaaccagtagagcggccacatgatgccgtacttgacccacgtaggcaccggtgcagggtcgatgtacgtcgacgcgacgtagagcagggacatgaccgcgatgtcaaaggccaggtacatgctgctacgaagcgccgagcgctcgaaacagtgcgcggggatggccttgcgcagcgtcccgatcgtgaacggaggcttctccacaggctgcctgttcgtcttgatagccat ctcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctgta gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc

We introduced the hairpin PmFAD2 construct into strain AP. Transgeniclines arising from the transformations with pSZ3372 (D2082) were assayedin lipid production media at pH5.0, the resulting profiles fromrepresentative clones are shown in Table 67. Among more than 400transformants we had screened, the strain AQ was isolated from thetransformant D2082.1, which produced <1% C18:2 during the initialprofile screening. Thus, this strain can be used to produce atriglyceride oil that is both high in oleic acid and low inpolyunsaturates. Due to the low polyunsaturate levels, the oil isexpected to have a high oxidative stability when tested via the AOCS Cd12b-92 method (see Section IV of this patent application andcorresponding examples).

TABLE 67 Lipid profile of representative clones arising fromtransformation with D2082 (pSZ3372) DNA. Sample ID C16:0 C18:0 C18:1C18:2 C18:3 α SAP_pH 5.0_glucose_day 5-T658; D2082-1 4.42 3.80 89.360.65 0.10 StrainAP_pH 5.0_glucose_day 5-T658; D2082-87 3.77 4.01 88.701.52 0.19 StrainAP_pH 5.0_glucose_day 5-T658; D2082-93 5.14 3.58 87.631.65 0.19 StrainAP_pH 5.0_glucose_day 5-T658; D2082-78 3.74 2.40 89.691.97 0.23 StrainAP_pH 5.0_glucose_day 5 4.10 3.77 83.55 6.41 0.40

Example 58 Generating High Oleic “Zero” Linoleic Strains by Knock-OutPrototheca Moriformis (PM) FAD2 AND FATA Genes and Over-Expression ofPMKASII Gene

Triacylglycerols in microalgae can be significantly enriched in levelsof oleate (C18:1) utilizing molecular genetic approaches, such as downregulating endogenous FATA1 and FADc genes and over-expression ofendogenous KASII activity. In this example, we focus our efforts oncombining these approaches into a single transgenic line. Constructsthat disrupt a single copy of the FATA1 allele while simultaneouslyoverexpressing the Prototheca moriformis KASII gene were introduced intodifferent Δfad2 lines, termed Strain R and Strain D (see genealogy inFIG. 24). The resulting strains, such as Strain AS and Strain AZproduces around 90% C18:1 with <0.05% C18:2.

Strain D and Strain R are Δfad2 lines that produce oils comprised of 0%C18:2, and between 76% to 87% C18:1, depending upon whether they aregrown in shake flasks or high cell density fermentations, respectively.To further elevate oleate levels in Strain D and Strain R, constructsthat disrupt a single copy of the FATA1 allele while simultaneouslyoverexpressing the P. moriformis KAS II gene were introduced in StrainD/Strain R via particle bombardment.

Construct to knock out FATA genes and over expression of PmKASII inS2530 background. Relevant restriction sites in the constructFATA1::CpACT-AtThic-nr:AMT03-S106SAD-PmKASII-nr::FATA1 (termed pSZ2276)are indicated in lowercase, bold and underlining and are 5′-3′ BspQ 1,Kpn I, Xba I, Mfe I, BamH I, EcoR I, Spe I, Asc I, Cla I, Sac I, BspQ I,respectively. BspQI sites delimit the 5′ and 3′ ends of the transformingDNA. Bold, lowercase sequences represent genomic DNA from UTEX1435 thatpermit targeted integration at FATA1 gene via homologous recombination.Proceeding in the 5′ to 3′ direction, the actin gene promoter from UTEX250 driving the expression of the Arabidopsis thaliana THIC gene isindicated by the boxed text. The initiator ATG and terminator TGA forAtTHIC are indicated by uppercase, bold italics while the coding regionis indicated in lowercase italics. The Chlorella vulgaris nitratereductase 3′ UTR is indicated by lowercase underlined text followed byan endogenous AMT03 promoter of Prototheca moriformis, indicated byboxed italics text. The Initiator ATG and terminator TGA codons of theP. moriformis KASII gene are indicated by uppercase, bold italics, whilethe remainder of the PmKASII coding region is indicated by bold italics.The Chlorella protothecoides UTEX 250 stearoyl-ACP desaturase transitpeptide is located between initiator ATG and the Asc I site. The C.vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the UTEX1435 FATA1 genomic region indicatedby bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ2276:(SEQ ID NO: 118) gctcttcggagtcactgtgccactgagttcgactggtagctgaatggagtcgctgctccactaaacgaattgtcagcaccgccagccggccgaggacccgagtcatagcgagggtagtagcgcgccatggcaccgaccagcctgcttgccagtactggcgtctcttccgcttctctgtggtcctctgcgcgctccagcgcgtgcgcttttccggtggatcatgcggtccgtggcgcaccgcagcggccgctgcccatgcagcgccgctgcttccgaacagtggcggtcagggccgcacccgcggtagccgtccgtccggaacccgcccaagagttttgggagcagcttgagccctgcaagatggcggaggacaagcgcatcttcctggaggagcaccggtgcgtggaggtccggggctgaccggccgtcgcattcaacgtaatcaatcgcatgatgatcagaggacacgaagtcttggtggcggtggccagaaacactgtccattgcaagggcatagggatgcgttccttcacctctcatttctcatttctgaatccctccctgctcactctttctcctcc

tggtctgcaacaacaagaaccactccgcccgccccaagctgcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGA ca a ttggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgattttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtg

gcccgcctgcccaccgcctcccgccgcgccgtgcgccgcgcctggtcccgcatcgcccgcg ggcgcgccgccgccgccgccgacgccaaccccgcccgccccgagcgccgcgtggtgatcaccggccagggcgtggtgacctccctgggccagaccatcgagcagttctactcctccctgctggagggcgtgtccggcatctcccagatccagaagttcgacaccaccggctacaccaccaccatcgccggcgagatcaagtccctgcagctggacccctacgtgcccaagcgctgggccaagcgcgtggacgacgtgatcaagtacgtgtacatcgccggcaagcaggccctggagtccgccggcctgcccatcgaggccgccggcctggccggcgccggcctggaccccgccctgtgcggcgtgctgatcggcaccgccatggccggcatgacctccttcgccgccggcgtggaggccctgacccgcggcggcgtgcgcaagatgaaccccttctgcatccccttctccatctccaacatgggcggcgccatgctggccatggacatcggcttcatgggccccaactactccatctccaccgcctgcgccaccggcaactactgcatcctgggcgccgccgaccacatccgccgcggcgacgccaacgtgatgctggccggcggcgccgacgccgccatcatcccctccggcatcggcggcttcatcgcctgcaaggccctgtccaagcgcaacgacgagcccgagcgcgcctcccgcccctgggacgccgaccgcgacggcttcgtgatgggcgagggcgccggcgtgctggtgctggaggagctggagcacgccaagcgccgcggcgccaccatcctggccgagctggtgggcggcgccgccacctccgacgcccaccacatgaccgagcccgacccccagggccgcggcgtgcgcctgtgcctggagcgcgccctggagcgcgcccgcctggcccccgagcgcgtgggctacgtgaacgcccacggcacctccacccccgccggcgacgtggccgagtaccgcgccatccgcgccgtgatcccccaggactccctgcgcatcaactccaccaagtccatgatcggccacctgctgggcggcgccggcgccgtggaggccgtggccgccatccaggccctgcgcaccggctggctgcaccccaacctgaacctggagaaccccgcccccggcgtggaccccgtggtgctggtgggcccccgcaaggagcgcgccgaggacctggacgtggtgctgtccaactccttcggcttcggcggccacaactcctgcgtgatcttccgcaagtacgacgagatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGA atcgatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaagacagggtggttggctggatggggaaacgctggtcgcgggattcgatcctgctgcttatatcctccctggaagcacacccacgactctgaagaagaaaacgtgcacacacacaacccaaccggccgaatatttgcttccttatcccgggtccaagagagactgcgatgcccccctcaatcagcatcctcctccctgccgcttcaatcttccctgcttgcctgcgcccgcggtgcgccgtctgcccgcccagtcagtcactcctgcacaggccccttgtgcgcagtgctcctgtaccctttaccgctccttccattctgcgaggccccctattgaatgtattcgttgcctgtgtggccaagcgggctgctgggcgcgccgccgtcgggcagtgctcggcgactttggcggaagccgattgttcttctgtaagccacgcgcttgctgctttgggaagagaagggggggggtactgaatggatgaggaggagaaggaggggtattggtattatctgagttgggtgaagagc

Construct to knock out FATA genes and over expression of PmKASII inS2532 background. Relevant restriction sites in the constructFATA1::CpACT-AtThic-nr:PmUAPA1-S106SAD-PmKASII-nr::FATA1 (termedpSZ2441) are indicated in lowercase, bold and underlining and are 5′-3′BspQ 1, Kpn I, Xba I, Mfe I, BamH I, EcoR V, Spe I, Asc I, Cla I, Sac I,BspQ I, respectively. BspQI sites delimit the 5′ and 3′ ends of thetransforming DNA. Bold, lowercase sequences represent genomic DNA fromUTEX1435 that permit targeted integration at FATA1 gene via homologousrecombination. Proceeding in the 5′ to 3′ direction, the actin genepromoter from UTEX 250 driving the expression of the A. thaliana THICgene is indicated by the boxed text. The initiator ATG and terminatorTGA for AtTHIC are indicated by uppercase, bold italics while the codingregion is indicated in lowercase italics. The Chlorella vulgaris nitratereductase 3′ UTR is indicated by lowercase underlined text followed byan endogenous UAPA1 promoter of Prototheca moriformis, indicated byboxed italics text. The Initiator ATG and terminator TGA codons of theP. moriformis KASII gene are indicated by uppercase, bold italics, whilethe remainder of the PmKASII coding region is indicated by bold italics.The Chlorella protothecoides UTEX 250 stearoyl-ACP desaturase transitpeptide is located between initiator ATG and the Asc I site. The C.vulgaris nitrate reductase 3′ UTR is again indicated by lowercaseunderlined text followed by the UTEX1435 FATA1 genomic region indicatedby bold, lowercase text.

Nucleotide sequence of transforming DNA contained in pSZ2441:(SEQ ID NO: 119) gctcttcggagtcactgtgccactgagttcgactggtagctgaatggagtcgctgctccactaaacgaattgtcagcaccgccagccggccgaggacccgagtcatagcgagggtagtagcgcgccatggcaccgaccagcctgcttgccagtactggcgtctcttccgcttctctgtggtcctctgcgcgctccagcgcgtgcgcttttccggtggatcatgcggtccgtggcgcaccgcagcggccgctgcccatgcagcgccgctgcttccgaacagtggcggtcagggccgcacccgcggtagccgtccgtccggaacccgcccaagagttttgggagcagcttgagccctgcaagatggcggaggacaagcgcatcttcctggaggagcaccggtgcgtggaggtccggggctgaccggccgtcgcattcaacgtaatcaatcgcatgatgatcagaggacacgaagtcttggtggcggtggccagaaacactgtccattgcaagggcatagggatgcgttccttcacctctcatttctcatttctgaatccctccctgctcactctttctcctcc

tggtctgcaacaacaagaaccactccgcccgccccaagctgcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtg

tgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcgggcgcgcc gccgccgccgccgacgccaaccccgcccgccccgagcgccgcgtggtgatcaccggccagggcgtggtgacctccctgggccagaccatcgagcagttctactcctccctgctggagggcgtgtccggcatctcccagatccagaagttcgacaccaccggctacaccaccaccatcgccggcgagatcaagtccctgcagctggacccctacgtgcccaagcgctgggccaagcgcgtggacgacgtgatcaagtacgtgtacatcgccggcaagcaggccctggagtccgccggcctgcccatcgaggccgccggcctggccggcgccggcctggaccccgccctgtgcggcgtgctgatcggcaccgccatggccggcatgacctccttcgccgccggcgtggaggccctgacccgcggcggcgtgcgcaagatgaaccccttctgcatccccttctccatctccaacatgggcggcgccatgctggccatggacatcggcttcatgggccccaactactccatctccaccgcctgcgccaccggcaactactgcatcctgggcgccgccgaccacatccgccgcggcgacgccaacgtgatgctggccggcggcgccgacgccgccatcatcccctccggcatcggcggcttcatcgcctgcaaggccctgtccaagcgcaacgacgagcccgagcgcgcctcccgcccctgggacgccgaccgcgacggcttcgtgatgggcgagggcgccggcgtgctggtgctggaggagctggagcacgccaagcgccgcggcgccaccatcctggccgagctggtgggcggcgccgccacctccgacgcccaccacatgaccgagcccgacccccagggccgcggcgtgcgcctgtgcctggagcgcgccctggagcgcgcccgcctggcccccgagcgcgtgggctacgtgaacgcccacggcacctccacccccgccggcgacgtggccgagtaccgcgccatccgcgccgtgatcccccaggactccctgcgcatcaactccaccaagtccatgatcggccacctgctgggcggcgccggcgccgtggaggccgtggccgccatccaggccctgcgcaccggctggctgcaccccaacctgaacctggagaaccccgcccccggcgtggaccccgtggtgctggtgggcccccgcaaggagcgcgccgaggacctggacgtggtgctgtccaactccttcggcttcggcggccacaactcctgcgtgatcttccgcaagtacgacgagatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGA atcgatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaagacagggtggttggctggatggggaaacgctggtcgcgggattcgatcctgctgcttatatcctccctggaagcacacccacgactctgaagaagaaaacgtgcacacacacaacccaaccggccgaatatttgcttccttatcccgggtccaagagagactgcgatgcccccctcaatcagcatcctcctccctgccgcttcaatcttccctgcttgcctgcgcccgcggtgcgccgtctgcccgcccagtcagtcactcctgcacaggccccttgtgcgcagtgctcctgtaccctttaccgctccttccattctgcgaggccccctattgaatgtattcgttgcctgtgtggccaagcgggctgctgggcgcgccgccgtcgggcagtgctcggcgactttggcggaagccgattgttcttctgtaagccacgcgcttgctgctttgggaagagaagggggggggtactgaatggatgaggaggagaaggaggggtattggtattatctgagttgggtgaagag c

Southern blot analysis of Strain AS and Strain AZ indicated that bothare PmFATA double knock-out mutants. Since the PmFAD2 disruptioncassettes contain a Carthamus tinctorius putative oleoyl-specificACP-thioesterase (CtOTE), the absence of the endogenous FATA genes seemsto be fully complemented by the expression of the CtOTE.

To determine the impact of FATA1 inactivation and over expression ofPmKASII gene on lipid composition in Δfad2 lines Strain D/Strain R, theprimary transformants of D1266/Strain D and D1415/Strain R were clonallypurified and grown under standard lipid production conditions at bothpH5.0 and pH7.0. The resulting profiles from the transgenic line arisingfrom transformation with pSZ2276 into Strain D are shown in Table 68,and transgenic lines arising from transformation with pSZ2441 intoStrain R are shown in Table 69.

As can be seen from Table 68, in Strain AZ at pH7.0, the combination offull activity of PmKASII driven by AMT03 and FATA1 knock results in verylow levels of C16:0 (2%). Meanwhile, the Carthamus tinctoriusthioesterase is also activated since it is also driven by AMT03promoter. We observe 7.8% C18:0 when Strain AZ is cultivated at pH7. AtpH5.0, decrease of the C16:0 level is largely contributed by the FATA1inactivation, although PmKASII can be partially activated since we runthe seed culture at pH6.8. The stearic level of Strain AZ is low atpH5.0 due to the low expression of the C. tinctorius TE. Overall, theoleic levels of Strain AZ exceed 85% (around 88%) at both pH7.0 andpH5.0.

TABLE 68 Fatty acid profiles in S1331, S2530 and S4266 at both pH 5.0and pH 7.0 Strains C16:0 C18:0 C18:1 C18:2 C20:1 Strain A_pH 5 26.6 3.360.5 6.7 0.07 Strain A_pH 7 28.3 4.1 58 6.5 0.06 Strain D_pH 5 17 3.677.1 0.01 0.14 Strain D_pH 7 19.5 5.3 72.6 0.01 0.09 Strain AZ_pH 5 4.12.36 88.5 0.04 3.1 Strain AZ_pH 7 2.1 7.8 87.9 0.01 0.5

In the transgenic line Strain AS, both CrTUB2 and PmUAPA1 promoters arepH unbiased, hence, as reported in Table 69, the lipid profile at pH5.0and pH7.0 are essentially same. Relative to Strain AZ, Strain ASproduces much less stearic acid. Although the palmitic level in StrainAS is bit higher than that in Strain AZ, the oleic level in Strain AS isabove 90%, which is the highest level we observed in the shake flaskexperiment.

TABLE 69 Fatty acid profiles in S1331, S2532 and S5204 at both pH 5.0and pH 7.0 Strains C16:0 C18:0 C18:1 C18:2 Strain A_pH 5 26.6 3.3 60.56.7 Strain A_pH 7 28.3 4.1 58 6.5 Strain R_pH 5 23.3 2.1 72.1 0.01Strain R_pH 7 23.4 2.3 71.9 0.01 Strain AS_pH 5 5.5 1.4 91.5 0.01 StrainAS_pH 7 5.6 1.6 91.3 0.01

Example 59 Complementation of FAD2 and FATA Knockout and KASIIOverexpression Generates a Unique Oil with High C18-2 and Low C18-3Levels

As described in Example 58, Strain AS was generated by knocking bothcopies of PmFATA1 in a Prototheca moriformis strain while simultaneouslyoverexpressing PmKASII gene into a Δfad2 line (Strain R). Strain R is aFAD2 (also known as FADc) knockout strain generated by insertion of aoleate-specific C. tinctorius acyl-ACP thioesterase (GenBank AccessionNo: AAA33019.1) into a high-lipid producing strain derived from UTEX1435, under the control of CrTUB2 promoter at the FAD2 locus. Strain ASand its parent, Strain R, have a disrupted endogenous PmFAD2-1 generesulting in no Δ12 specific desaturase activity manifested as 0% C18:2(linoleic acid) levels in both nitrogen-rich seed and nitrogen-poorlipid production conditions. Lack of C18:2 in Stain AS (and its parentStrain R) resulted in growth defects which could be partially mitigatedby exogenous addition of linoleic acid in the seed stage. However, forindustrial applications, exogenous addition of linoleic acid isexpensive. Complementation of Strain R (and a second Δfad2 strain) withPmFAD2-1 restored C18:2 levels back to wild type levels and alsoresulted in rescued growth characteristics during seed and lipidproduction without any linoleic supplementation.

In the present example we demonstrate that:

-   -   In trans expression of fatty acid desaturase-2 gene from        Prototheca moriformis (PmFad2-1) under the control of a pH        inducible PmAMT3 promoter results in functional complementation        of PmFAD2-1 with restored growth and C18:2 levels in Δfad2,        Δfata1 strain AS;    -   Complementation of Strain AS is conditional/inducible and occurs        at pH 7.0 when the AMT3 promoter is actively driving the        expression of PmFAD2-1 as opposed to pH 5.0 when the AMT3        promoter is inactive; and    -   Over expression of PmFAD2-1 at pH 7.0 results in strains        with >20% C18:2 levels. The fatty acid profile of these high        C18:2 strains mimic canola oil closely except that the new oil        has 5 fold less C18:3 than the canola oil (10%). The elevated        C18:2 levels are seen only in strains derived from Strain AS        overexpressing PmFAD2-1 since overexpression of the same gene in        wild-type (i.e., non-engineered) control Strain Z does not        result in higher C18:2 levels.

Construct used for the expression of the Prototheca moriformis fattyacid desaturase 2 (PmFAD2-1) in Δfad2 strains Strain AS and StrainZ—[pSZ2721]. Δfad2 Δfata1 Strain AS and Strain Z were transformed withthe construct pSZ2721. The sequence of the transforming DNA is providedbelow. Relevant restriction sites in the construct pSZ2721(6S::CpACT-ScMEL1-CvNR::PmAMT3-PmFAD2-1-CvNR::6S) are indicated inlowercase, underlined and bold, and are from 5′-3′ BspQ 1, KpnI, Xba I,Mfe I, BamH I, EcoR I, Spe I, Cla I, Sac I, BspQ I, respectively. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences represent genomic DNA from UEX 1435 that permitstargeted integration of PmFAD2-1 at the 6S locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the actin (ACT)gene promoter from UTEX 250 driving the expression of the Saccharomycescerevisiae MEL1 gene is indicated by the boxed text. The initiator ATGand terminator TGA for ScMEL1 are indicated by uppercase, bold italicswhile the coding region is indicated in lowercase italics. The Chlorellavulgaris nitrate reductase 3′ UTR is indicated by lowercase underlinedtext followed by an endogenous AMT03 promoter of Prototheca moriformis,indicated by boxed italics text. The Initiator ATG and terminator TGAcodons of the PmFAD2-1 are indicated by uppercase, bold italics, whilethe remainder of the gene is indicated by bold italics. The C. vulgarisnitrate reductase 3′ UTR is again indicated by lowercase underlined textfollowed by the UTEX 1435 6S genomic region indicated by bold, lowercasetext. The final construct was sequenced to ensure correct reading framesand targeting sequences.

Nucleotide sequence of transforming DNA contained in plasmid pSZ2721:(SEQ ID NO: 120) gctcttcggagtcactgtgccactgagttcgactggtagctgaatggagtcgctgctccactaaacgaattgtcagcaccgccagccggccgaggacccgagtcatagcgagggtagtagcgcgccatggcaccgaccagcctgcttgccagtactggcgtctcttccgcttctctgtggtcctctgcgcgctccagcgcgtgcgcttttccggtggatcatgcggtccgtggcgcaccgcagcggccgctgcccatgcagcgccgctgcttccgaacagtggcggtcagggccgcacccgcggtagccgtccgtccggaacccgcccaagagttttgggagcagcttgagccctgcaagatggcggaggacaagcgcatcttcctggaggagcaccggtgcgtggaggtccggggctgaccggccgtcgcattcaacgtaatcaatcgcatgatgatcagaggacacgaagtcttggtggcggtggccagaaacactgtccattgcaagggcatagggatgcgttccttcacctctcatttctcatttctgaatccctccctgctcactctttctcctcc

ccctgaagggcgtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctcc TGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcccgcgtctcgaacagagcgcgcagaggaacgctgaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcga

gcgcaaggccatccccgcccactgcttcgagcgctccgccctgcgctcctccatgtacctggccttcgacatcgccgtgatgtccctgctgtacgtggcctccacctacatcgaccccgcccccgtgcccacctgggtgaagtacggcgtgatgtggcccctgtactggttcttccagggcgccttcggcaccggcgtgtgggtgtgcgcccacgagtgcggccaccaggccttctcctcctcccaggccatcaacgacggcgtgggcctggtgttccactccctgctgctggtgccctactactcctggaagcactcccaccgccgccaccactccaacaccggctgcctggacaaggacgaggtgttcgtgcccccccaccgcgccgtggcccacgagggcctggagtgggaggagtggctgcccatccgcatgggcaaggtgctggtgaccctgaccctgggctggcccctgtacctgatgttcaacgtggcctcccgcccctacccccgcttcgccaaccacttcgacccctggtcccccatcttctccaagcgcgagcgcatcgaggtggtgatctccgacctggccctggtggccgtgctgtccggcctgtccgtgctgggccgcaccatgggctgggcctggctggtgaagacctacgtggtgccctacctgatcgtgaacatgtggctggtgctgatcaccctgctgcagcacacccaccccgccctgccccactacttcgagaaggactgggactggctgcgcggcgccatggccaccgtggaccgctccatgggcccccccttcatggacaacatcctgcaccacatctccgacacccacgtgctgcaccacctgttctccaccatcccccactaccacgccgaggaggcctccgccgccatccgccccatcctgggcaagtactaccagtccgactcccgctgggtgggccgcgccctgtgggaggactggcgcgactgccgctacgtggtgcccgacgcccccgaggacgactccgccctgtggttccacaagTAG atcgatagatctcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaagagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaagacagggtggttggctggatggggaaacgctgctggtcgcgggattcgatcctgctgcttatatcctccctggaagcacacccacgactctgaagaagaaaacgtgcacacacacaacccaaccggccgaatatttgcttccttatcccgggtccaagagagactgcgatgcccccctcaatcagcatcctcctccctgccgcttcaatcttccctgcttgcctgcgcccgcggtgcgccgtctgcccgcccagtcagtcactcctgcacaggccccttgtgcgcagtgctcctgtaccctttaccgctccttccattctgcgaggccccctattgaatgtattcgttgcctgtgtggccaagcgggctgctgggcgcgccgccgtcgggcagtgctcggcgactttggcggaagccgattgttcttctgtaagccacgcgcttgctgctttgggaagagaagggggggggtactgaatggatgaggaggagaaggaggggtattggtattatctgagttgggt gaagagc

To determine its impact on growth and fatty acid profiles, the aboveconstruct was transformed independently into a Δfad2 Δfata1 Strain AS orwild type Strain Z. Primary transformants were clonally purified andgrown under low-nitrogen lipid production conditions at pH7.0 (AMT3promoter active) and pH5.0 (AMT3 promoter inactive) for Strain AStransformants or at pH7.0 for Strain Z transformants. The resultingprofiles from a set of representative clones arising fromtransformations are shown in Tables 70-73 respectively.

Expression of endogenous PmFad2-1 driven by AMT3 promoter at pH 7.0, inStrain AS resulted in Δ12 specific desaturase activity with completerestoration of C18:2 fatty acid levels of the base strain A (Table 70).No such Δ12 specific desaturase activity and thus no significant C18:2restoration is detected when the lipid production is run at pH 5.0 whenthe AMT3 promoter is inactive (Table 71).

Interestingly, lipid production in complemented Strain AS strains at pH7.0 results in several strains with 2 fold or more increase in C18:2levels. The resulting strains produce an oil profile that is similar toCanola oil except that the new oil has less C18:3 levels than thecommercially available canola oil (Table 72). The increase in C18:2 isnot seen in wild type (Strain Z) strains transformed with the same AMT3driven PmFAD2-1.

While we have seen other strains with high C18:2 levels, all of themwere associated with growth defects in seed as well as lipid productionmedia. Here, however, we have been able to increase the C18:2 levels ina targeted manner without any detrimental effect on the growth ofresulting strains. While Δfad2 strain R and Δfad2 Δfata1 strain AS growvery poorly and hardly reach an OD750 of 10-20 in 42 hours, complementedStrain AS (D1673) lines grow very rapidly in the same time span andreach OD750 between 50-80.

Thus, it can be seen that we were able to produce cell oils with fattyacid profiles of less than 10% linolenic acid yet >20% linoleic acid(indeed we achieved <2% linolenic acid and >20% linoleic acid). It issurprising that C18:2 levels are elevated only in Strain AS, which hasalmost 90% C18:1 levels as compared to Strain Z with only 57% C18:1levels, suggests excess availability of substrate C18:1 in the ER is akey to boost C18:2 levels. Since Prototheca has evolved to utilize C18:1onto TAGS very efficiently, in wild type situations most likely thesubstrate leaves the ER very rapidly before being further desaturated byFAD2 enzymes. This limitation may be overcome in strains like Strain ASwith very high C18:1 levels that likely stays available for desaturationby PmFAD2-1.

TABLE 70 Fatty acid profile in representative complemented (D1673) andparent Strain AS lines at pH 7.0 transformed with pSZ2721 (PmFAD2-1)DNA. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3a AS; T533; D1673-16;pH 7.0 0.49 6.33 2.44 66.53 21.36 1.38 AS; T533; D1673-17; pH 7.0 0.446.02 2.25 68.97 19.53 1.36 AS; T533; D1673-02; pH 7.0 0.38 5.92 2.3071.01 17.77 1.30 AS; T533; D1673-03; pH 7.0 0.38 5.83 2.31 71.31 17.451.29 AS; T533; D1673-10; pH 7.0 0.38 5.63 2.21 71.72 17.37 1.23 AS; pH7.0 0.30 5.59 1.63 90.88 0.10 0.00 AT; pH 7.0 1.34 27.99 3.54 55.48 9.070.79

TABLE 71 Fatty acid profile in same representative complemented (D1673)and parent Strain AS lines at pH 5.0 transformed with pSZ2721 (PmFAD2-1)DNA. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3a AS; T533; D1673-16;0.47 5.16 1.76 90.94 0.06 0.18 pH 5.0 AS; T533; D1673-17; 0.45 4.97 1.7291.32 0.05 0.00 pH 5.0 AS; T533; D1673-02; 0.46 5.20 1.75 90.94 0.050.18 pH 5.0 AS; T533; D1673-03; 0.41 4.93 1.65 89.92 1.56 0.16 pH 5.0AS; T533; D1673-10; 0.45 4.97 1.69 89.96 1.35 0.16 pH 5.0 AS; pH 5.00.39 5.67 1.36 91.13 0.00 0.00 AT; pH 5.0 1.03 24.69 3.30 63.47 5.800.38

TABLE 72 Fatty acid profile of a stable D1673 line along with basestrain Z and Canola oil. Sample ID C16:0 C18:0 C18:1 C18:2 C18:3 α C20:1pH 5 Strain Z 27.54 3.29 57.91 7.17 0.59 0.10 pH 7 Strain Z 27.92 3.0958.30 6.71 0.59 0.07 pH 7; AS; T533; D1673.5.2-1 4.43 1.31 70.32 20.301.72 0.75 pH 7; AS; T533; D1673.5.2-2 4.55 1.26 67.53 22.17 1.82 1.22 pH7; AS; T533; D1673.5.2-3 4.34 1.29 69.51 20.78 1.65 1.01 pH 7; AS; T533;D1673.5.2-4 4.81 1.26 68.08 21.53 1.77 1.06 pH 7; AS; T533; D1673.5.2-54.61 1.30 68.02 21.57 1.74 1.17 pH 7; AS; T533; D1673.5.2-6 4.36 1.3068.88 21.16 1.68 1.10 pH 7; AS; T533; D1673.5.2-7 4.38 1.28 69.30 21.081.70 0.97 pH 7; AS; T533; D1673.5.2-8 4.87 1.27 68.44 20.87 1.83 1.14Canola Oil 4.00 2.00 62.00 22.00 10.00 1.00

TABLE 73 Fatty acid profile in Strain Z at pH 5.0 and pH 7.0 andrepresentative derivative transgenic lines at pH 7.0 transformed withpSZ2721 (PmFAD2-1) DNA. The lines are sorted by C18:2 levels. Sample IDC14:0 C16:0 C18:0 C18:1 C18:2 C18:3a Z; T573; D1791-23; pH 7.0 1.4529.96 3.28 54.72 7.99 0.66 Z; T573; D1791-6; pH 7.0 1.73 30.25 2.4855.01 7.74 0.69 Z; T573; D1791-17; pH 7.0 1.41 29.00 3.42 55.77 7.640.68 Z; T573; D1791-14; pH 7.0 1.48 29.82 3.45 55.22 7.56 0.67 Z; T573;D1791-8; pH 7.0 2.30 37.15 2.54 47.62 7.44 0.67 Z; T573; D1791-2; pH 7.01.38 29.29 3.45 56.10 7.12 0.63 Z; T573; D1791-10; pH 7.0 1.46 29.303.39 56.16 7.11 0.60 Z; T573; D1791-5; pH 7.0 1.45 29.45 3.36 56.15 7.020.61 Z; T573; D1791-11; pH 7.0 1.43 29.52 3.44 55.99 7.01 0.60 Z; T573;D1791-13; pH 7.0 1.41 28.96 3.46 56.47 7.01 0.62 Z; pH 7.0 1.41 27.763.45 57.71 7.17 0.58 Z; pH 5.0 1.49 28.19 3.27 58.04 6.65 0.57

Example 60 Combinatorial Expression of Mid-Chain Thioesterases andKetoacyl Synthases to Generate Oils with Highly Elevated and BalancedC10:0 AND C12:0 Fatty Acid Levels

In this example we describe two molecular approaches to generate oilswith highly elevated and balanced C10:0 and C12:0 fatty acids in aclassically mutagenized high-oil-yielding derivative of UTEX 1435,Strain BA. Resulting transgenic strains co-express two distinctmid-chain specific thioesterases, the broad specificity C10:0-C14:0Cuphea wrightii FATB2 thioesterase (expressed in Stain BA), andpredominantly C10:0—specific Cuphea hookeriana FATB2 thioesterase (partof incoming vectors). In addition, D1550 transformants express C.wrightii KASIV elongase gene integrated at a neutral genomic site,Thi4b, (vector pSZ2424), while D1681 transformants—C. wrightii KASAIelongase as a part of an endogenous KASI disruption cassette (vectorpSZ2746). The use of different KASI activities of plant origin incombination with the exogenous thioesterases resulted in a significantincrease in overall C10-C12 levels as well as improved C10:0 specificityof the C. hookeriana thioesterase. The best strain synthesized about 85%total C10:0-C12:0 fatty acids with balanced levels of about 42% C10:0and ca. 44% C12:0 fatty acids, respectively, less than 4% C14:0, andless than 1.5% C8:0. The results show that selection of FATB and KASgenes can give rise to an oil with at least 50% total saturates withcapric and lauric acids balanced to within 20% (or even to within 15%,or 10%).

Relevant restriction sites in pSZ2424 are indicated in lowercase, boldand underlining text and are 5′-3′ Pme I, Kpn I, Xba I, Mfe I, Eco RI,Spe I, Xho I, Hind III, SnaBI, Spe I, Asc I, Xho I, Eco RI, Sac I, BspQI, respectively. Pme I and BspQI sites delimit the 5′ and 3′ ends of thetransforming DNA. Bold, lowercase sequences represent genomic DNA fromUTEX1435 that permit targeted integration at Thi4b locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the C. reinhardtiiB-tubulin promoter driving the expression of the neomycinphosphotransferase gene (NeoR, conferring the ability of cells to growon G418) is indicated by boxed text. The initiator ATG and terminatorTGA for NeoR are indicated by uppercase, bold italics while the codingregion is indicated in lowercase italics. The Chlorella vulgaris nitratereductase 3′ UTR is indicated by lowercase underlined text. Next is theAmt03 promoter of Prototheca moriformis indicated by boxed lowercasetext driving the expression of Cuphea hookeriana KASIV gene (ChKASIV)indicated in lowercase italics. The initiator ATG and terminator TGA forChKASIV are indicated by uppercase, bold italics. The Chlorella vulgarisnitrate reductase 3′ UTR is indicated by lowercase underlined text. Nextis the Amt03 promoter of Prototheca moriformis indicated by boxedlowercase text driving the expression of Cuphea hookeriana FATB2 gene(ChFATB2) fused to plastid transit peptide sequence derived fromPrototheca moriformis FAD gene indicated in lowercase italics. Theinitiator ATG and terminator TGA for ChFATB2 are indicated by uppercase,bold italics. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the UTEX1435 Thi4bflanking sequence.

Nucleotide sequence of transforming DNA contained in pSZ2424:(SEQ ID NO: 121) gtttaaacccctcaactgcgacgctgggaaccttctccgggcaggcgatgtgcgtgggtttgcctccttggcacggctctacaccttcgagtacgccatgaggcggtgatggctgtggctgtgccccacttcgtccagggacggcaagtccatcatctgcatgcttggtgcgacgctacagcagtccctctgcagcagaggagcacgactttggccatttcacgcactcgagtgtacacaattcatttttcttaaagtaaatgactgctgattgaccagatgctgtaacgctgatttcgctccagatcgcacagtcacagattgcgaccatgttgctgcgtctgaaaatctggattccgaattcgaccctggcgctccatccatgcaacagatggcgacacttgttacaattcctgtcgcccatcggcatggagcaggtccacttagatccccgatcacccacgcgcatctcgctaatagtcattcattcgtgtcttcgatcaaagtcaggtgagtatgcatggatcttggttgacgatgcggtatgggtttgcgccgctgactgcagggtctgtccaaggcaagccaacccagctcctctcctcgacaatactctcgcagacaaagccagccacttgccatccagattgccaataaactcaatcatggcttctgtcatgccatccatgggtctgatgaatggtcacgctcgtgtcctgaccgttccccagcctctggcgtcccctgccccgcccaccagcc

gactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttc TGAcaattggcagcagcagtcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgg

tgcacctggctggtcgccgcgtgcatgcccacctccagcgacaacgacccccgctcgctgtcccacaagcgcctgcgcctgagccgccgccgccgcaccctgagctcgcactgctccctgcgcggcagcaccttccagtgcctggacccctgcaaccagcagcgcttcctgggcgacaacggcttcgcgtcgctgttcggctccaagcccctgcgcagcaaccgcggccacctgcgcctgggccgcacctcgcactccggcgaggtgatggccgtcgcgatgcagcccgcccaggaggtgagcaccaacaagaagcccgcgaccaagcagcgccgcgtggtcgtgaccggcatgggcgtcgtgacccccctgggccacgaccccgacgtgtattataacaacctgctggacggcatctcgggcatctccgagatcgagaacttcgactgcagccagttccccacccgcatcgccggcgagatcaagtcgttctccaccgacggctgggtcgcgcccaagttcagcgagcgcatggacaagttcatgctgtatatgctgaccgccggcaagaaggcgctggccgacggcggcatcaccgaggacgcgatgaaggagctgaacaagcgcaagtgcggcgtgctgatcggctcgggcctgggcggcatgaaggtcttctccgacagcatcgaggccctgcgcacctcgtataagaagatctcccccttctgcgtgcccttcagcaccaccaacatgggctcggcgatcctggcgatggacctgggctggatgggccccaactattccatcagcaccgcgtgcgccacctcgaacttctgcatcctgaacgcggccaaccacatcatcaagggcgaggcggacatgatgctgtgcggcggctccgacgccgcggtgctgcccgtcggcctgggcggcttcgtggcctgccgcgcgctgagccagcgcaacaacgaccccaccaaggcctcgcgcccctgggactccaaccgcgacggcttcgtcatgggcgagggcgcgggcgtgctgctgctggaggagctggagcacgccaagaagcgcggcgcgaccatctatgccgagttcctgggcggcagcttcacctgcgacgcgtatcacatgaccgagccccaccccgagggcgccggcgtcatcctgtgcatcgagaaggcgctggcccagtcgggcgtgtcccgcgaggacgtgaactatatcaacgcgcacgccaccagcacccccgcgggcgacatcaaggagtatcaggccctggcgcactgcttcggccagaactcggagctgcgcgtcaactccaccaagagcatgatcggccacctgctgggcggcgccggcggcgtggaggcggtcgccgtggtccaggcgatccgcaccggctggatccaccccaacatcaacctggaggaccccgacgagggcgtggacgccaagctgctggtcggccccaagaaggagaagctgaaggtgaaggtcggcctgtcgaactccttcggcttcggcggccacaacagctcgatcctgttcgcgccctgcaac TGActcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgatttgcgagttgctagagcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagta

gcctccgttcacgatcgggacgctgcgcaaggccatccccgcgcactgtttcgagcgctcggcgcttcgtgg g c gcg cc cagctgcccgactggagccgcctgctgaccgccatcaccaccgtgttcgtgaagtccaagcgccccgacatgcacgaccgcaagtccaagcgccccgacatgctggtggacagcttcggcctggagtccaccgtgcaggacggcctggtgttccgccagtccttctccatccgctcctacgagatcggcaccgaccgcaccgccagcatcgagaccctgatgaaccacctgcaggagacctccctgaaccactgcaagagcaccggcatcctgctggacggcttcggccgcaccctggagatgtgcaagcgcgacctgatctgggtggtgattaagatgcagatcaaggtgaaccgctaccccgcctggggcgacaccgtggagatcaacacccgcttcagccgcctgggcaagatcggcatgggccgcgactggctgatctccgactgcaacaccggcgagatcctggtgcgcgccaccagcgcctacgccatgatgaaccagaagacccgccgcctgtccaagctgccctacgaggtgcaccaggagatcgtgcccctgttcgtggacagccccgtgatcgaggactccgacctgaaggtgcacaagttcaaggtgaagaccggcgacagcatccagaagggcctgacccccggctggaacgacctggacgtgaaccagcacgtgtccaacgtgaagtacatcggctggatcctggagagcatgcccaccgaggtgctggagacccaggagctgtgctccctggccctggagtaccgccgcgagtgcggccgcgactccgtgctggagagcgtgaccgccatggaccccagcaaggtgggcgtgcgctcccagtaccagcacctgctgcgcctggaggacggcaccgccatcgtgaacggcgccaccgagtggcgccccaagaacgccggcgccaacggcgccatctccaccggcaagaccagcaacggcaactccgtgtccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGActcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctgta gaattc tcca gagctccagcgccatgccacgccttttgatggcttcaagtacgataacggtgttggattgtgcgtttgttgcgtagtgtgcatggcttagaataatgcagttggatttcttgctcacggcaatgtcggcttgtccgcaggttcaaccccatttcggagtctcaggtcagccgcgcaatgaccagccgctacttcaaggacttgcacgacaacgccgaggtgagctatgtttaggccttgagtgaaaattgtcgtcgaagcatattcgcgctccgcgatagcatccaagcaaaatgtcaagtgcgttccgatttgcgtccgcaggtcgatgttgtgatcgtcggtgccggatccgccggtctgtcctgcgcttacgagctgaccaagcaccccgacgtccgggtacgcgagctgagattcgattggacataaactgaaaatgaaatcttttggagaaatgtaagggtctcaagcggtgctcgattgcaagaaattggtcgtcccccactccgcaggtcgccatcatcgagcagggcgttgcacctggtggcggcgcctggctggggggacagctgttctcggccatgtgtgtacgtagaagggtggatttcggatggtttcgttgcacagctgtttgtcaatgatttgtcttagactattgccgatgtttctaaatgttttaggagctatgatatgtctgcaggcgactgaagagc

Relevant restriction sites in pSZ2746 are indicated in lowercase, boldand underlining text and are 5′-3′ BspQ 1, Kpn I, Xba I, Mfe I, HindIII, AscI, Spe I, Xho I, Eco RI, Nde I, Sna BI, Xho I, Hind III, Sac I,BspQ I, respectively. BspQI sites delimit the 5′ and 3′ ends of thetransforming DNA. Bold, lowercase sequences represent genomic DNA fromUTEX1435 that permit targeted integration (and knockout) at the KASIlocus via homologous recombination. Proceeding in the 5′ to 3′direction, the C. reinhardtii B-tubulin promoter driving the expressionof the neomycin phosphotransferase gene (NeoR, conferring the ability ofcells to grow on G418) is indicated by boxed text. The initiator ATG andterminator TGA for NeoR are indicated by uppercase, bold italics whilethe coding region is indicated in lowercase italics. The Chlorellavulgaris nitrate reductase 3′ UTR is indicated by lowercase underlinedtext. Next is the UAPA1 promoter of Prototheca moriformis indicated byboxed lowercase text driving the expression of Cuphea hookeriana FATB2gene (ChFATB2) fused to plastid transit peptide sequence derived fromPrototheca moriformis FAD gene indicated in lowercase italics. Theinitiator ATG and terminator TGA for ChFATB2 are indicated by uppercase,bold italics. The B. braunii cd191 3′UTR is indicated by lowercaseunderlined text. Next is the Amt03 promoter of Prototheca moriformisindicated by boxed lowercase text driving the expression of Cupheawrightii KASAI gene indicated by lowercase italics fused to Protothecamoriformis SAD1 plastid transit peptide sequence. The C. wrightii KASAIsequence is in lowercase italics and is delineated by initiator ATG andterminator TGA. The C. vulgaris nitrate reductase 3′ UTR is againindicated by lowercase underlined text followed by the UTEX1435 KASIflanking sequence.

Nucleotide sequence of transforming DNA contained in pSZ2746:(SEQ ID NO: 122)gctcttcgctcaccgcgtgaattgctgtcccaaacgtaagcatcatcgtggctcggtcacgcgatcctggatccggggatcctagaccgctggtggagagcgctgccgtcggattggtggcaagtaagattgcgcaggttggcgaagggagagaccaaaaccggaggctggaagcgggcacaacatcgtattattgcgtatagtagagcagtggcagtcgcatttcgaggtccgcaacggatctcgcaagctcgctacgctcacagtaggagaaaggggaccactgcccctgccagaatggtcgcgaccctctccctcgccggccccgcctgcaacacgcagtgcgtatccggcaagcgggctgtcgccttcaaccgcccccatgttggcgtccgggctcgatcaggtgcgctgaggggggtttggtgtgcccgcgcctctgggcccgtgtcggccgtgcggacgtggggccctgggcagtggatcagcagggtttgcgtgcaaatgcctataccggcgattgaatagcgatgaacgggatacggttgcgctcactccatgcccatgcgaccccgtttctg

ggctcccccgccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttc TGAcaattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacct

gggacgctgcgcaaggccatccccgcgcactgtttcgagcgctcggcgcttcgtg ggc g c g cccagctgcccgactggagccgcctgctgaccgccatcaccaccgtgttcgtgaagtccaagcgccccgacatgcacgaccgcaagtccaagcgccccgacatgctggtggacagcttcggcctggagtccaccgtgcaggacggcctggtgttccgccagtccttctccatccgctcctacgagatcggcaccgaccgcaccgccagcatcgagaccctgatgaaccacctgcaggagacctccctgaaccactgcaagagcaccggcatcctgctggacggcttcggccgcaccctggagatgtgcaagcgcgacctgatctgggtggtgattaagatgcagatcaaggtgaaccgctaccccgcctggggcgacaccgtggagatcaacacccgcttcagccgcctgggcaagatcggcatgggccgcgactggctgatctccgactgcaacaccggcgagatcctggtgcgcgccaccagcgcctacgccatgatgaaccagaagacccgccgcctgtccaagctgccctacgaggtgcaccaggagatcgtgcccctgttcgtggacagccccgtgatcgaggactccgacctgaaggtgcacaagttcaaggtgaagaccggcgacagcatccagaagggcctgacccccggctggaacgacctggacgtgaaccagcacgtgtccaacgtgaagtacatcggctggatcctggagagcatgcccaccgaggtgctggagacccaggagctgtgctccctggccctggagtaccgccgcgagtgcggccgcgactccgtgctggagagcgtgaccgccatggaccccagcaaggtgggcgtgcgctcccagtaccagcacctgctgcgcctggaggacggcaccgccatcgtgaacggcgccaccgagtggcgccccaagaacgccggcgccaacggcgccatctccaccggcaagaccagcaacggcaactccgtgtccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGActcgagagcgtccagcgtgtgggatgaagggtgcgatggaacggggctgccgccccccctctgggcatctagctctgcaccgcacgccaggaagcccaagccaggccccgtcacactccctcgctgaagtgttccccccctgccccacactcatccaggtatcaacgccatcatgttctacgtccccgtcatcttcaactccctggggagcgggcgccgc

atgtcggcgtgccccgcgatgactggcagggcccctggggcacgtcgctccggacggccagtcgccacccgcctgaggta cg tattccagtgcctggtggccagctgcatcgacccctgcgaccagtaccgcagcagcgccagcctgagcttcctgggcgacaacggcttcgccagcctgttcggcagcaagcccttcatgagcaaccgcggccaccgccgcctgcgccgcgccagccacagcggcgaggccatggccgtggccctgcagcccgcccaggaggccggcaccaagaagaagcccgtgatcaagcagcgccgcgtggtggtgaccggcatgggcgtggtgacccccctgggccacgagcccgacgtgttctacaacaacctgctggacggcgtgagcggcatcagcgagatcgagaccttcgactgcacccagttccccacccgcatcgccggcgagatcaagagcttcagcaccgacggctgggtggcccccaagctgagcaagcgcatggacaagttcatgctgtacctgctgaccgccggcaagaaggccctggccgacggcggcatcaccgacgaggtgatgaaggagctggacaagcgcaagtgcggcgtgctgatcggcagcggcatgggcggcatgaaggtgttcaacgacgccatcgaggccctgcgcgtgagctacaagaagatgaaccccttctgcgtgcccttcgccaccaccaacatgggcagcgccatgctggccatggacctgggctggatgggccccaactacagcatcagcaccgcctgcgccaccagcaacttctgcatcctgaacgccgccaaccacatcatccgcggcgaggccgacatgatgctgtgcggcggcagcgacgccgtgatcatccccatcggcctgggcggcttcgtggcctgccgcgccctgagccagcgcaacagcgaccccaccaaggccagccgcccctgggacagcaaccgcgacggcttcgtgatgggcgagggcgccggcgtgctgctgctggaggagctggagcacgccaagaagcgcggcgccaccatctacgccgagttcctgggcggcagcttcacctgcgacgcctaccacatgaccgagccccaccccgagggcgccggcgtgatcctgtgcatcgagaaggccctggcccaggccggcgtgagcaaggaggacgtgaactacatcaacgcccacgccaccagcaccagcgccggcgacatcaaggagtaccaggccctggcccgctgcttcggccagaacagcgagctgcgcgtgaacagcaccaagagcatgatcggccacctgctgggcgccgccggcggcgtggaggccgtgaccgtggtgcaggccatccgcaccggctggattcaccccaacctgaacctggaggaccccgacaaggccgtggacgccaagctgctggtgggccccaagaaggagcgcctgaacgtgaaggtgggcctgagcaacagcttcggcttcggcggccacaacagcagcatcctgttcgccccctgcaacgtg TGActcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatgg a aagcttgagctccacctgcatccgcctggcgctcgaggacgccggcgtctcgcccgacgaggtcaactacgtcaacgcgcacgccacctccaccctggtgggcgacaaggccgaggtgcgcgcggtcaagtcggtctttggcgacatgaagggcatcaagatgaacgccaccaagtccatgatcgggcactgcctgggcgccgccggcggcatggaggccgtcgccacgctcatggccatccgcaccggctgggtgcaccccaccatcaaccacgacaaccccatcgccgaggtcgacggcctggacgtcgtcgccaacgccaaggcccagcacaaaatcaacgtcgccatctccaactccttcggcttcggcgggcacaactccgtcgtcgcctttgcgcccttccgcgagtaggcggagcgagcgcgcttggctgaggagggaggcggggtgcgagccctttggctgcgcgcgatactctccccgcacgagcagactccacgcgcctgaatctacttgtcaacgagcaaccgtgtgttttgtccgtggccattcttattatttctccgactgtggccgtactctgtttggctgtgcaagcacc gaagagcc  

Fatty acids profiles from representative shake flask cultures of stablelines derived from D1550 transformants are shown in Table 74. Twoindependent genetic lineages yielded strains with high and balancedlevels of C10-C12:0 fatty acids.

TABLE 74 Fatty acid profiles in S5050 and derivative transgenic linesgenerated after transformation with pSZ2424 DNA. Fatty Acid (area %)Strain C8:0 C10:0 C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 Total SaturatesStrain BA 0.32 14.96 43.84 16.60 10.49 0.54 9.64 2.49 86.75D1550-29.C4.A2 4.02 32.82 40.98 7.37 5.06 0.40 5.61 2.37 90.65D1550-29.C4.A3 4.50 33.93 40.23 7.09 4.91 0.36 5.38 2.30 91.02D1550-29.C4.A4 3.57 34.31 41.04 6.86 4.90 0.36 4.98 2.56 91.04D1550-29.C4.A5 4.66 34.23 39.68 6.96 4.90 0.36 5.55 2.32 90.79D1550-29.C6.E2 3.59 35.44 40.49 6.32 4.74 0.34 4.94 2.63 90.92D1550-29.C6.E3 3.60 35.55 40.90 6.33 4.67 0.34 4.66 2.52 91.39D1550-29.C6.E4 BB 3.97 35.85 40.23 6.26 4.65 0.34 4.83 2.51 91.30D1550-29.C6.E5 4.02 35.19 39.89 6.59 4.79 0.34 5.12 2.60 90.82D1550-29-1.14 3.30 39.62 40.04 5.16 4.04 0.30 3.49 2.67 92.46D1550-29-1.2 3.12 39.50 40.22 5.13 3.86 0.29 3.42 2.82 92.12D1550-29-1.12 3.26 39.36 39.91 5.13 4.15 0.30 3.73 2.77 92.11D1550-29-1.17 3.25 39.21 40.21 5.22 4.11 0.30 3.70 2.67 92.30D1550-29-1.39 4.12 38.44 39.23 5.83 4.25 0.30 3.96 2.46 92.17D1550-29-1.35 BC 3.60 38.06 39.79 5.89 4.35 0.29 3.98 2.58 91.98D1550-29-1.7 3.15 39.18 40.04 5.24 4.05 0.32 3.68 2.88 91.98D1550-29-1.1 2.87 38.29 40.76 5.20 4.20 0.31 3.79 2.86 91.63

Next, we analyzed the performance of D1681 strains that were constructedusing the KASI replacement strategy. Interestingly, unlike D1550transformants, the D1681 strains demonstrated greater variability infatty acid profiles (Table 75). In addition, the D1681 derived lines hadlower C8:0 levels than what we observed in the D1550 derived transgeniclines suggesting a direct role of C. wrightii KASAI in improving C10:0specificity of C. hookeriana FATB2 thioesterase.

TABLE 75 Fatty acid profiles in Strain BA and derivative transgeniclines generated after transformation with pSZ2746 DNA. Fatty Acid (area%) Total Strain C8:0 C10:0 C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 SaturatesStrain BA 0.89 13.17 40.52 17.53 11.60 0.59 11.38 2.95 84.30 D1681.3.7-2BD 1.44 31.83 44.97 6.52 4.83 0.30 6.53 2.45 89.89 D1681.3.7-10 1.8431.41 43.64 6.90 5.15 0.31 7.08 2.46 89.25 D1681.3.7-12 BE 1.85 31.6443.50 6.76 5.08 0.31 7.16 2.49 89.14 D1681.3.4-1 1.29 31.61 45.92 6.654.49 0.29 6.20 2.46 90.25 D1681.3.4-6 BF 1.48 32.26 45.11 6.55 4.56 0.296.23 2.41 90.25 D1681.3.4-9 1.42 31.22 45.40 6.93 4.69 0.30 6.49 2.4789.96 D1681.3.8-1 1.35 27.72 44.72 8.78 5.97 0.37 7.36 2.51 88.91D1681.3.8-4 1.44 27.51 44.34 8.72 6.05 0.36 7.84 2.51 88.42 D1681-2.1-370.64 34.80 47.17 4.84 3.81 0.31 4.37 2.43 91.57 D1681-2.1-34 0.62 35.2647.07 4.77 3.77 0.30 4.22 2.36 91.79 D1681-2.1-28 BG 0.64 35.99 46.804.65 3.68 0.29 4.02 2.34 92.05 D1681-2.1-12 0.67 34.78 47.21 4.94 3.790.34 4.30 2.35 91.73 D1681.2.4-1.3 BH 0.57 33.95 47.73 4.93 3.39 0.030.24 3.96 92.60 D1681.2.4-1.4 0.56 36.71 47.55 4.86 3.26 0.03 0.24 3.6192.97 D1681.2.4-1.12 BI 1.89 34.72 44.70 6.32 4.03 0.02 0.27 5.18 91.68D1681.2.4-1.2 1.73 36.43 44.25 5.57 4.09 0.03 0.32 4.55 92.10

Eight strains representing D1550 and D1681 families (from Tables 74-75)were subsequently evaluated in high cell density fermentations as shownin Table 76. Fermentations resulted in oils with a slightly improvedmid-chain profile or the balance of C10-C12:0 fatty acid levels comparedto the lab scale fermentation. Strain BE evaluated in two independentfermentations demonstrated superior profile reaching 85.2% C10-C12:0fatty acid levels, 3.5% C14:0 levels, and ca. 1.2% C8:0 fatty acidlevels, and accumulated over 92% total saturates.

TABLE 76 End-point fatty acid profiles in D1550 and D1681 derivativetransgenic lines subjected to high cell density fermentation. Strain BBBC BG BH BI BF BE Run 130067 130196 130197 130291 130292 130253 130246PF13029 Fatty C8:0 5.3 4.62 4.62 0.54 1.53 1.59 2.1 1.19 Acid C10:036.19 36.16 36.16 33.24 40 40.46 40.94 41.59 Profile C12:0 39.07 38.7738.77 47.65 43.09 42.39 41.25 43.6 (Area %) C14:0 5.31 5.18 5.18 5 4.624.42 4.2 3.49 C16:0 3.72 3.9 3.9 3.4 2.83 2.63 2.8 2.28 C18:0 0.24 0.280.28 0.27 0.22 0.32 0.28 0.15 C18:1 6.12 6.79 6.79 5.88 4.95 5.34 5.84.76 C18:2 2.43 2.76 2.76 2.49 1.95 2.05 1.89 1.96 C10-C14 80.57 80.1180.11 85.89 87.71 87.27 86.39 88.68 C10-C12 75.26 74.93 74.93 80.8983.09 82.85 82.19 85.19 Total Saturates 89.83 88.91 88.91 90.1 92.2991.81 91.57 92.3

Example 61 Tag Regiospecificity in UTEX1435 by Expression of CupheaPSR23 LPAAT2 and LPAAT3 Genes

In Example 43, we demonstrated that the expression of 2 different1-acyl-sn-glycerol-3-phosphate acyltransferases (LPAATs), the LPAAT2 andLPAAT3 genes from Cuphea PSR23 (CuPSR23) in the UTEX1435 derivativestrain S2014 resulted in elevation of C10:0, C12:0 and C14:0 fatty acidslevels. In this example we provide evidence that Cuphea PSR23 LPAAT2exhibits high specificity towards incorporating C10:0 fatty acids atsn-2 position in TAGs. The Cuphea PSR23 LPAAT3 specifically incorporatesC18:2 fatty acids at sn-2 position in TAGs.

Composition and properties of Prototheca moriformis (UTEX 1435)transgenic strain B, transforming vectors pSZ2299 and pSZ2300 thatexpress CuPSR23 LPAAT2 and LPAAT3 genes, respectively, and theirsequences were described previously.

To determine the impact of Cuphea PSR23 LPAAT genes on the resultingfatty acid profiles we have taken advantage of Strain B whichsynthesizes both mid chain and long chain fatty acids at relatively highlevels. As shown in Table 77, the expression of the LPAAT2 gene (D1520)in Strain B resulted in increased C10-C12:0 levels (up to 12% in thebest strain, D1520.3-7) suggesting that this LPAAT is specific for midchain fatty acids. Alternatively, expression of the LPAAT3 gene resultedin a relatively modest increase, (up to 5% in the best strain,D1521.28-7) indicating it has little or no impact on mid-chain levels.

TABLE 77 Fatty acid profiles of Strain B and representative transgeniclines transformed with pSZ2299 (D1520) and pSZ2300 (D1521) DNA. FattyAcid (area %) C10: C12: C14: C16: C18: C18: C18: C10- Total Strain C8:00 0 0 0 0 1 2 C12 Saturates Strain B 0.09 4.95 29.02 15.59 12.55 1.2727.93 7.60 33.97 63.47 D1520.8-6 0.00 6.71 31.15 15.80 13.04 1.42 24.326.56 37.86 68.12 D1520.13-4 0.00 6.58 30.96 16.14 13.34 1.25 24.32 6.2737.54 68.27 D1520.19-4 0.00 7.53 32.94 16.64 12.63 1.17 21.96 6.11 40.4770.91 D1520.3-7 0.06 9.44 36.26 16.71 11.44 1.28 18.41 5.59 45.70 75.19D1521.13-8 0.00 6.21 33.13 16.70 12.30 1.18 20.84 8.70 39.34 69.52D1521.18-2 0.00 5.87 31.91 16.46 12.60 1.22 22.14 8.59 37.78 68.06D1521.24-8 0.00 5.75 31.47 16.13 12.60 1.42 23.31 8.22 37.22 67.37D1521.28-7 0.00 6.28 32.82 16.33 12.27 1.43 21.98 7.91 39.10 69.13

To determine if expression of the Cuphea PSR23 LPAAT genes affectedregiospecificity of fatty acids at the sn-2 position, we analyzed TAGsfrom representative D1520 and D1521 strains utilizing the porcinepancreatic lipase method. See Example 2. As demonstrated in Table 78,the Cuphea PSR23 LPAAT2 gene shows remarkable specificity towards C10:0fatty acids and appears to incorporate 50% more C10:0 fatty acids intothe sn-2 position. The Cuphea PSR23 LPAAT3 gene appears to actexclusively on C18:2 fatty acids, resulting in redistribution of C18:2fatty acids onto sn-2 position. Accordingly, microbial triglyceride oilswith sn-2 profiles of greater than 15% or 20% C10:0 or C18:2 fatty acidsare obtainable by introduction of an exogenous LPAAT gene havingcorresponding specificity.

TABLE 78 TAG and sn-2 fatty acid profiles in oils of parental S2014strain and the progeny strains expressing Cuphea PSR23 LPAAT2 (BJ) andLPAAT3 (BK) genes. Strain Strain B Strain BI (D1520.3-7) Strain BK(D1521.13-8) Analysis TAG Profile sn-2 Profile TAG Profile sn-2 ProfileTAG Profile sn-2 Profile Fatty C8:0 0 0 0.1 0 0 0 Acid C10:0 12 14.2 1124.9 6.21 6.3 (area C12:0 42.8 25.1 40.5 24.3 33.13 19.5 %) C4:0 12.110.4 16.3 10 16.7 11.8 C6:0 7.3 1.3 10.2 1.4 12.3 3 C8:0 0.7 0.2 0.9 0.61.18 0.5 C8:1 18.5 36.8 15.4 29.2 20.84 36.3 C8:2 5.8 10.9 4.9 8.7 8.720.9 C18:3a 0.6 0.8 0.4 0.8 0.48 1.2 C10-C14 66.9 49.7 67.8 59.2 56.037.6 C10-C12 54.8 39.3 51.5 49.2 39.3 25.8

Example 62 Introduction of Heterologous Thioesterases into aHeterologous KAS-Expressing Prototheca Moriformis Strain

Here we demonstrate that heterologous fatty acyl-ACP thioesterasesexhibit altered thioesterase specificity when combined with aheterologous plant KASI gene, Cuphea wrightii β-ketoacyl-ACP synthase(KAS), CwKASA1, in P. moriformis (UTEX 1435) transgenic strain, S5818.S5818 is a transgenic strain expressing a thioesterase chimera fromCinnamomum camphora and Umbellularia californica, CcFATB2-UcFATB2chimera B, at the 6S locus and additionally expressing the Cupheawrightii KAS, CwKASA1, at the pLOOP locus. The addition of theCcFATB2-UcFATB2 chimera B and CwKASA1 genes leads to an S5818 fatty acidprofile with 45% C12:0 and 14% C14:0. Five different constructs encodingthioesterases that were previously shown to exhibit predominantly C14:0thioesterase activity and with less pronounced C12:0 thioesteraseactivity in P. moriformis were introduced into S5818 in an effort toincrease C14:0 and C12:0 levels in this background. However,introduction of the five different C14:0 thioesterases into S5818 led tounexpected but significant increases in C12:0 fatty acid levels (>50%overall) with only modest increases in C14:0 fatty acid levels (<20%overall). This result suggests that the KASI-FATB thioesterasecombination exhibits a unique activity not displayed when either gene isintroduced separately. The results demonstrate that combination ofheterologous KAS genes with heterologous thioesterases in oleaginouscells can be used to produce fatty acid profiles not exhibited byintroduction of either gene alone. Furthermore, introduction ofheterologous KASs may be an important and fruitful approach forrevealing novel specificities of additional heterologous thioesterases.

Strain S5818 generation. S5818 was created by two successivetransformations. The UTEX1435 base strain, S3150 (Strain Z above), wastransformed with pSZ2448 (6SA::CrTUB2-ScSUC2-CvNR:PmAMT3-CpSAD1tpExt-CcFATB2-UcFATB2-chimeraB-ExtA-CvNR::6SB),encoding the CcFATB2-UcFATB2 chimera B thioesterase targeting the 6Slocus, to yield strain S4954. S4954 produces ˜32% C12:0 and ˜16% C14:0fatty acid levels (Table 62-1). S4954 was subsequently transformed withpSZ2229 (pLOOP::CrTUB2-NeoR-CvNR:PmAMT3-PmSADtp_CwKASAI-CvNR::pLOOP),encoding the C. wrightii KASA1 gene targeting the pLOOP locus, to yieldstrain S5818. S5818 produces ˜45% C12:0 and ˜14% C14:0 fatty acid levels(Table 79).

TABLE 79 Fatty acid profiles of S3150, S4954, and S5818. Sample ID C10:0C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 Strain Z 0 0.05 1.49 28.83 3.2457.87 6.27 S4954 0.17 31.52 16.39 9.81 1.19 32.14 7.19 S5818 0.34 45.1613.77 8.54 0.81 24.63 5.38

Identification of C14:0 thioesterases. In an effort to increase C14:0fatty acid levels, and to a lesser degree C12:0 fatty acid levels,several thioesterases that were found to exhibit C14:0 and C12:0thioesterase activity in P. moriformis were cloned into vectors forintroduction into S5818. The Cuphea hyssopifolia thioesterase ChsFATB3was discovered by us as part of efforts to identify novel thioesterasesby sequencing the mature, plant oilseeds of C. hyssopifolia. Although C.hyssopifolia seeds exhibit ˜84% C12:0 and ˜5% C14:0 fatty acid levels,the ChsFATB3 thioesterase we identified exhibits strong C14:0thioesterase activity when expressed in S3150 (up to ˜34% C14:0). Aversion of ChsFATB3 in which we optimized the putative plastid-targetingtransit peptide, named pSADD1tp_trimmed:ChsFATB3, similarly exhibitedstrong C14:0 thioesterase activity (˜33% C14:0; Table 80).

TABLE 80 Fatty acid profiles of Cuphea hyssopifolia seeds and S3150 withintroduction of ChsFATB3 or CpSAD1tp_trimmed:ChsFATB3. Sample ID C8:0C10:0 C12:0 C14:0 C16:0 C18:0 C18:1 C18:2 Cuphea hyssopifolia seeds 0.246.53 83.69 5.13 1.10 0.12 0.00 1.74 S3150 0.00 0.00 0.05 1.49 28.83 3.2457.87 6.27 S3150 + ChsFATB3 (T537; D1701-48) 0.00 0.00 8.09 33.66 26.461.57 23.75 5.3 S3150 + CpSAD1tp_trimmed:ChsFATB3 0.00 0.14 7.25 33.3227.04 1.57 24.37 5.12 (T580; D1813-8)

Similarly, we also identified the Cuphea heterophylla thioesteraseChtFATB1a as part of our efforts to identify novel thioesterases bysequencing the mature, plant oil seeds of C. heterophylla. Although C.heterophylla seeds exhibit ˜44% C10:0, ˜40% C12:0 fatty acid levels, andonly ˜4% C14:0, the transit peptide optimized version of the ChtFATB1athioesterase we identified, CpSAD1tp_trimmed:ChtFATB1a, exhibits strongC14:0 thioesterase activity when expressed in S3150 (up to ˜35% C14:0;Table 81).

TABLE 81 Fatty acid profiles of Cuphea heterophylla seeds and S3150 withintroduction of CpSAD1tp_trimmed:ChtFATB1a. Sample ID C8:0 C10:0 C12:0C14:0 C16:0 C18:0 C18:1 C18:2 Cuphea heterophylla seeds 3.50 44.27 40.044.26 1.22 0.25 2.21 3.56 S3150 0.00 0.00 0.05 1.49 28.83 3.24 57.87 6.27S3150 + CpSAD1tp_trimmed:ChtFATB1a 0.00 0.15 13.18 35.16 24.1 1.19 18.876.02 (T580; D1811-44)

A published Cuphea palustris C14:0 thioesterase, CpalFATB2, was alsointroduced into S5818 (vide infra).

Introduction of C14:0 thioesterases into S5818. Five constructs weregenerated using C14:0 thioesterases for introduction into S5818 (Table82).

TABLE 82 Constructs engineered for introduction into S5818. D# pSZ#Construct D2104 pSZ3390DAO1b::PmHXT1-ScarMel1-CvNR:PmUAPA1noSacI-CpSAD1tpExt-CpaIFATB2FLAGExtA-CvNR::DAO1bD2202 pSZ3493DAO1b5¹::PmHXT1-ScarMEL1-CvNR:PmAMT3-ChsFATB3-CvNR::DAO1b3¹ D2203pSZ3494DAO1b5¹::PmHXT1-ScarMEL1-CvNR:PmAMT3-CpSAD1tp_trimmed:ChsFATB3-CvNR::DAO1b3¹D2204 pSZ3495DAO1b5¹::PmHXT1-ScarMEL1-CvNR:PmAMT3-CpSAD1tp_trimmed:ChtFATB1a-CvNR::DAO1b3¹D2235 pSZ3531 THI4A::PmHXT1-ScarMel1 -CpEF1a:PmUAPA1noSacI-CpSAD1tpExt-CpaIFATB2FLAGExtA-CvNR::THI4A

pSZ3390 and pSZ3531 introduce the CpalFATB2 thioesterase gene into theDAO1b and THI4A loci, respectively, under the control of thepH5-responsive UAPA1 promoter. pSZ3493, pSZ3494, and pSZ3495 introduceChsFATB3, CpSAD1tp_trimmed:ChsFATB3, and CpSAD1tp trimmed:ChtFATB1a,respectively, into the DAO1b locus under the control of thepH7-responsive AMT3 promoter. Transgenic strains were selected for theability to grow on melibiose. Cell culture, lipid production, and fattyacid analysis were all carried out as previously described. Thetransforming DNA for pSZ3390, pSZ3493, pSZ3494, pSZ3495, and pSZ3531 areprovided below.

pSZ3390: pSZ3390 can be written as DAO1b::PmHXT1-ScarMel1-CvNR:PmUAPA1noSacI-CpSAD1tpExt-CpalFATB2FLAGExtA-CvNR::DOA1b.The relevant restriction sites in the construct from 5′-3′, BspQI, KpnI,SpeI, SnaBI, XhoI, EcoRI, SpeI, HindIII, SacI, BspQI, respectively, areindicated in lowercase, bold, and underlined. BspQI sites delimit the 5′and 3′ ends of the transforming DNA. Bold, lowercase sequences at the 5′and 3′ end of the construct represent genomic DNA from UTEX 1435 thattarget integration to the DAO1b locus via homologous recombination.Proceeding in the 5′ to 3′ direction, the selection cassette has the P.moriformis HXT1 promoter driving the expression of the S. carlbergensisMEL1 gene (conferring the ability to grow on melibiose) and theChlorella vulgaris Nitrate Reductase (NR) gene 3′ UTR. The promoter isindicated by lowercase, boxed text. The initiator ATG and terminator TGAfor ScarMEL1 are indicated by bold, uppercase italics, while the codingregion is indicated with lowercase italics. The 3′UTR is indicated bylowercase, underlined text. The second cassette containing theCpSAD1tpExt-CpalFATB2FLAGExtA gene, fused to the heterologous Chlorellaprotothecoides SAD1 plastid-targeting transit peptide, is driven by theP. moriformis UAPA1 pH5-responsive promoter and has the Chlorellavulgaris Nitrate Reductase (NR) gene 3′ UTR. In this cassette, the UAPA1promoter is indicated by lowercase, boxed text. The initiator ATG andterminator TGA for the CpSAD1tpExt-CpalFATB2FLAGExtA gene are indicatedin bold, uppercase italics, while the coding region is indicated bylowercase italics. The 3′ UTR is indicated by lowercase, underlinedtext.

pSZ3390 transforming construct: (SEQ ID NO: 123) gaagagcGCCCAATGTTTAAACagcccgcaccctcgttgatctgggagccctgcgcagccccttaaatcatctcagtcaggtttctgtgttcaactgagcctaaagggctttcgtcatgcgcacgagcacacgtatatcggccacgcagtttctcaaaagcggtagaacagttcgcgagccctcgtaggtcgaaaacttgcgccagtactattaaattaaattaattgatcgaacgagacgcgaaacttttgcagaatgccaccgagtttgcccagagaatgggagtggcgccattcaccatccgcctgtgcccggcttgattcgccgagacgatggacggcgagaccagggagcggcttgcgagccccgagccggtagcaggaacaatgatcgacaatcttcctgtccaattactggcaaccattagaaagagccggagcgcgttgaaagtctgcaatcgagtaatttttcgatacgtcgggcctgctgaaccctaaggctccggactttgtttaaggcgatccaagatgcacgcggccccaggcacgtatctcaagcacaaaccccagccttagtttcgagactttgggagatagcgaccgatatctagtttggcattttgtatattaattacctcaagcaatggagcgctctgatgcggtgcagcgtcggctgcagcacctggcagtggcgctagggtcgccctatcgctcggaacctggtcagctggctcccgcctcctgc

ctccctgaagggcgtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctccTGAtacgtactcgaggcagcagcagtcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaa

ctcggcgttcaatgcccgctgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcgctgccatcgccagcgaggtccccgtggccaccacctccccccgggcgcaccccaaggcgaacggcagcgcggtgtcgctgaagtcgggctccctggagacccaggaggacaagacgagcagctcgtccccccccccccgcacgttcatcaaccagctgcccgtgtggagcatgctgctgtcggcggtgaccacggtcttcggcgtggccgagaagcagtggcccatgctggaccgcaagtccaagcgccccgacatgctggtcgagcccctgggcgtggaccgcatcgtctacgacggcgtgagcttccgccagtcgttctccatccgcagctacgagatcggcgccgaccgcaccgcctcgatcgagacgctgatgaacatgttccaggagacctccctgaaccactgcaagatcatcggcctgctgaacgacggcttcggccgcacgcccgagatgtgcaagcgcgacctgatctgggtcgtgaccaagatgcagatcgaggtgaaccgctaccccacgtggggcgacaccatcgaggtcaacacgtgggtgagcgcctcgggcaagcacggcatgggccgcgactggctgatctccgactgccacaccggcgagatcctgatccgcgcgacgagcgtctgggcgatgatgaaccagaagacccgccgcctgtcgaagatcccctacgaggtgcgccaggagatcgagccccagttcgtcgactccgcccccgtgatcgtggacgaccgcaagttccacaagctggacctgaagacgggcgacagcatctgcaacggcctgaccccccgctggacggacctggacgtgaaccagcacgtcaacaacgtgaagtacatcggctggatcctgcagtcggtccccaccgaggtgttcgagacgcaggagctgtgcggcctgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagagcgtcacggccatggacccctcgaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgcggacatcgtgaagggccgcaccgagtggcgccccaagaacgccggcgccaagggcgccatcctgacgggcaagaccagcaacggcaactcgatctccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGAaagcttgcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctcccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagctggagctcagcgtctgcgtgttgggagctggagtcgtgggcttgacgacggcgctgcagctgttgcaggatgtgcctggcgtgcgcgttcacgtcgtggctgagaaatatggcgacgaaacgttgacggctggggccggcgggctgtggatgccatacgcattgggtacgcggccattggatgggattgataggcttatggagggataatagagtttttgccggatccaacgcatgtggatgcggtatcccggtgggctgaaagtgtggaaggatagtgcattggctattcacatgcactgcccaccccttttggcaggaaatgtgccggcatcgttggtgcaccgatggggaaaatcgacgttcgaccactacatgaagatttatacgtctgaagatgcagcgactgcgggtgcgaaacggatgacggtttggtcgtgtatgtcacagcatgtgctggatcttgcgggctaactccccctgccacggcccattgcaggtgtcatgttgactggagggtacgacctttcgtccgtcaaattcccagaggaggacccgctctgggccgacattgtgcccactgaagagc 

pSZ3493, pSZ3494, and pSZ3495: pSZ3493 can be written asDOA1b5′::PmHXT1-ScarMEL1-CvNR:PmAMT3-ChsFATB3-CvNR::DOA1b3′. pSZ3494 canbe written as DOA1b5′::PmHXT1-ScarMEL1-CvNR:PmAMT3-CpSAD1tptrimmed:ChsFATB3-CvNR::DOA1b3′. pSZ3495 can be written asDOA1b5′::PmHXT1-ScarMEL1-CvNR:PmAMT3-CpSAD1tp_trimmed:ChtFATB1a-CvNR::DOA1b3′. The sequences of the three constructs differonly in the sequence of the thioesterase gene. The full transformingsequence for pSZ3493 is displayed in SEQ ID NO:124. The sequences of theCpSAD1tp_trimmed: ChsFATB3 and CpSAD1tp_trimmed:ChtFATBla genes alone,which take the place of ChsFATB3 from pSZ3493 in the pSZ3494 and pSZ3495sequences, are displayed in SEQ ID NOs:125 and 126, respectively, alongwith flanking restriction sites.

The relevant restriction sites in the pSZ3493 construct from 5′-3′,BspQI, KpnI, SpeI, SnaBI, XhoI, EcoRI, SpeI, XhoI, SacI, BspQI,respectively, are indicated in lowercase, bold, and underlined. BspQIsites delimit the 5′ and 3′ ends of the transforming DNA. Bold,lowercase sequences at the 5′ and 3′ end of the construct representgenomic DNA from UTEX 1435 that target integration to the DAO1b locusvia homologous recombination. Proceeding in the 5′ to 3′ direction, theselection cassette has the P. moriformis HXT1 promoter driving theexpression of the S. carlbergensis MEL1 gene (conferring the ability togrow on melibiose) and the Chlorella vulgaris Nitrate reductase (NR)gene 3′ UTR. The promoter is indicated by lowercase, boxed text. Theinitiator ATG and terminator TGA for ScarMEL1 are indicated by bold,uppercase italics, while the coding region is indicated with lowercaseitalics. The 3′UTR is indicated by lowercase, underlined text. Thesecond cassette is comprised of the ChsFATB3 gene driven by the P.moriformis AMT3 pH7-responsive promoter and with the Chlorella vulgarisNitrate Reductase (NR) gene 3′ UTR. In this cassette, the AMT3 promoteris indicated by lowercase, boxed text. The initiator ATG and terminatorTGA for the ChsFATB3 gene are indicated in bold, uppercase italics,while the coding region is indicated by lowercase italics. The 3′ UTR isindicated by lowercase, underlined text.

pSZ3493 transforming construct: (SEQ ID NO: 124) gaagagcGCCCAATGTTTAAACagcccgcaccctcgttgatctgggagccctgcgcagccccttaaatcatctcagtcaggtttctgtgttcaactgagcctaaagggctttcgtcatgcgcacgagcacacgtatatcggccacgcagtttctcaaaagcggtagaacagttcgcgagccctcgtaggtcgaaaacttgcgccagtactattaaattaaattaattgatcgaacgagacgcgaaacttttgcagaatgccaccgagtttgcccagagaatgggagtggcgccattcaccatccgcctgtgcccggcttgattcgccgagacgatggacggcgagaccagggagcggcttgcgagccccgagccggtagcaggaacaatgatcgacaatcttcctgtccaattactggcaaccattagaaagagccggagcgcgttgaaagtctgcaatcgagtaatttttcgatacgtcgggcctgctgaaccctaaggctccggactttgtttaaggcgatccaagatgcacgcggccccaggcacgtatctcaagcacaaaccccagccttagtttcgagactttgggagatagcgaccgatatctagtttggcattttgtatattaattacctcaagcaatggagcgctctgatgcggtgcagcgtcggctgcagcacctggcagtggcgctagggtcgccctatcgctcggaacctggtcagctggctcccgcctcctgc

ctccctgaagggcgtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctccTGAtacgtactcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggttIgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaa

cggcacctcccccaagcccggcaagttcggcaactggcccacctccctgtccgtgcccttcaagtccaagtccaaccacaacggcggcttccaggtgaaggccaacgcctccgcccgccccaaggccaacggctccgccgtgtccctgaagtccggctccctggacacccaggaggacacctcctcctcctcctcccccccccgcaccttcatcaaccagctgcccgactggtccatgctgctgtccgccatcaccaccgtgttcgtggccgccgagaagcagtggaccatgctggaccgcaagtccaagcgccccgacatgctgatggaccccttcggcgtggaccgcgtggtgcaggacggcgccgtgttccgccagtccttctccatccgctcctacgagatcggcgccgaccgcaccgcctccatcgagaccctgatgaacatcttccaggagacctccctgaaccactgcaagtccatcggcctgctgaacgacggcttcggccgcacccccgagatgtgcaagcgcgacctgatctgggtggtgaccaagatgcacgtggaggtgaaccgctaccccacctggggcgacaccatcgaggtgaacacctgggtgtccgagtccggcaagaccggcatgggccgcgactggctgatctccgactgccacaccggcgagatcctgatccgcgccacctccatgtgcgccatgatgaaccagaagacccgccgcttctccaagttcccctacgaggtgcgccaggagctggccccccacttcgtggactccgcccccgtgatcgaggactaccagaagctgcacaagctggacgtgaagaccggcgactccatctgcaacggcctgaccccccgctggaacgacctggacgtgaaccagcacgtgaacaacgtgaagtacatcggctggatcctggagtccgtgcccaccgaggtgttcgagacccaggagctgtgcggcctgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagtccgtgaccgccatggacccctccaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgccgacatcgccaagggccgcaccaagtggcgccccaagaacgccggcaccaacggcgccatctccaccggcaagacctccaacggcaactccatctccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGActcgaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaAAGCTGTATAGGGATAACAGGGTAAT gagctcagcgtctgcgtgttgggagctggagtcgtgggcttgacgacggcgctgcagctgttgcaggatgtgcctggcgtgcgcgttcacgtcgtggctgagaaatatggcgacgaaacgttgacggctggggccggcgggctgtggatgccatacgcattgggtacgcggccattggatgggattgataggcttatggagggataatagagtttttgccggatccaacgcatgtggatgcggtatcccggtgggctgaaagtgtggaaggatagtgcattggctattcacatgcactgcccaccccttttggcaggaaatgtgccggcatcgttggtgcaccgatggggaaaatcgacgttcgaccactacatgaagatttatacgtctgaagatgcagcgactgcgggtgcgaaacggatgacggtttggtcgtgtatgtcacagcatgtgctggatcttgcgggctaactccccctgccacggcccattgcaggtgtcatgttgactggagggtacgacctttcgtccgtcaaattcccagaggaggacccgctctgggccgacattgtgcccactgaagagc  CpSAD1tp_trimmed:ChsFATB3 (from pSZ3494):(SEQ ID NO: 125) actagt AACAATGgccaccgcctccaccttctccgccttcaacgcccgctgcggcgacctgcgccgctccgccggctccggcccccgccgccccgcccgccccctgcccgtgcgcgccgccatcaacgcctccgcccgccccaaggccaacggctccgccgtgtccctgaagtccggctccctggacacccaggaggacacctcctcctcctcctcccccccccgcaccttcatcaaccagctgcccgactggtccatgctgctgtccgccatcaccaccgtgttcgtggccgccgagaagcagtggaccatgctggaccgcaagtccaagcgccccgacatgctgatggaccccttcggcgtggaccgcgtggtgcaggacggcgccgtgttccgccagtccttctccatccgctcctacgagatcggcgccgaccgcaccgcctccatcgagaccctgatgaacatcttccaggagacctccctgaaccactgcaagtccatcggcctgctgaacgacggcttcggccgcacccccgagatgtgcaagcgcgacctgatctgggtggtgaccaagatgcacgtggaggtgaaccgctaccccacctggggcgacaccatcgaggtgaacacctgggtgtccgagtccggcaagaccggcatgggccgcgactggctgatctccgactgccacaccggcgagatcctgatccgcgccacctccatgtgcgccatgatgaaccagaagacccgccgcttctccaagttcccctacgaggtgcgccaggagctggccccccacttcgtggactccgcccccgtgatcgaggactaccagaagctgcacaagctggacgtgaagaccggcgactccatctgcaacggcctgaccccccgctggaacgacctggacgtgaaccagcacgtgaacaacgtgaagtacatcggctggatcctggagtccgtgcccaccgaggtgttcgagacccaggagctgtgcggcctgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagtccgtgaccgccatggacccctccaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgccgacatcgccaagggccgcaccaagtggcgccccaagaacgccggcaccaacggcgccatctccaccggcaagacctccaacggcaactccatctccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGA ctcgag  CpSAD1tp_trimmed:ChtFATB1a (from pSZ3495): (SEQ ID NO: 126) actagtAACAATGgccaccgcctccaccttctccgccttcaacgcccgctgcggcgacctgcgccgctccgccggctccggcccccgccgccccgcccgccccctgcccgtgcgcgccgccatcaacgcctccgcccaccccaaggccaacggctccgccgtgaacctgaagtccggctccctggagacccaggaggacacctcctcctcctccccccccccccgcaccttcatcaagcagctgcccgactggggcatgctgctgtccaagatcaccaccgtgttcggcgccgccgagcgccagtggaagcgccccggcatgctggtggagcccttcggcgtggaccgcatcttccaggacggcgtgttcttccgccagtccttctccatccgctcctacgagatcggcgccgaccgcaccgcctccatcgagaccctgatgaacatcttccaggagacctccctgaaccactgcaagtccatcggcctgctgaacgacggcttcggccgcacccccgagatgtgcaagcgcgacctgatctgggtggtgaccaagatccaggtggaggtgaaccgctaccccacctggggcgacaccatcgaggtgaacacctgggtgtccgagtccggcaagaacggcatgggccgcgactggctgatctccgactgccgcaccggcgagatcctgatccgcgccacctccgtgtgggccatgatgaaccgcaagacccgccgcctgtccaagttcccctacgaggtgcgccaggagatcgccccccacttcgtggactccgcccccgtgatcgaggacgacaagaagctgcacaagctggacgtgaagaccggcgactccatccgcaagggcctgaccccccgctggaacgacctggacgtgaaccagcacgtgaacaacgtgaagtacatcggctggatcctgaagtccgtgcccgccgaggtgttcgagacccaggagctgtgcggcgtgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagtccgtgaccgccatggacaccgccaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgccgacatcaccatcggccgcaccgagtggcgccccaagaacgccggcgccaacggcgccatctccaccggcaagacctccaacgagaactccgtgtccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGA ctcgag  

pSZ3531: pSZ3531 can be written asTHI4A::PmHXT1-ScarMel1-CpEF1a:PmUAPA1noSacI-CpSAD1tpExt-CpalFATB2FLAGExtA-CvNR::THI4A.The relevant restriction sites in the construct from 5′-3′, BspQI, KpnI,SpeI, SnaBI, EcoRV, EcoRI, SpeI, HindIII, SacI, BspQI, respectively, areindicated in lowercase, bold, and underlined. BspQI sites delimit the 5′and 3′ ends of the transforming DNA. Bold, lowercase sequences at the 5′and 3′ end of the construct represent genomic DNA from UTEX 1435 thattarget integration to the THI4A locus via homologous recombination.Proceeding in the 5′ to 3′ direction, the selection cassette has the P.moriformis HXT1 promoter driving the expression of the S. carlbergensisMEL1 gene (conferring the ability to grow on melibiose) and theChlorella protothecoides EF1A gene 3′ UTR. The promoter is indicated bylowercase, boxed text. The initiator ATG and terminator TGA for ScarMEL1are indicated by bold, uppercase italics, while the coding region isindicated with lowercase italics. The 3′UTR is indicated by lowercase,underlined text. The second cassette containing theCpSAD1tpExt-CpalFATB2FLAGExtA gene, fused to the heterologous Chlorellaprotothecoides SAD1 plastid-targeting transit peptide, is driven by theP. moriformis UAPA1 pH5-responsive promoter and has the Chlorellavulgaris Nitrate Reductase (NR) gene 3′ UTR. In this cassette, the UAPA1promoter is indicated by lowercase, boxed text. The initiator ATG andterminator TGA for the CpSAD1tpExt-CpalFATB2FLAGExtA gene are indicatedin bold, uppercase italics, while the coding region is indicated bylowercase italics. The 3′ UTR is indicated by lowercase, underlinedtext.

pSZ3531 transforming construct: (SEQ ID NO: 127) gaagagcGCCCAATGTTTAAACCcctcaactgcgacgctgggaaccttctccgggcaggcgatgtgcgtgggtttgcctccttggcacggctctacaccgtcgagtacgccatgaggcggtgatggctgtgtcggttgccacttcgtccagagacggcaagtcgtccatcctctgcgtgtgtggcgcgacgctgcagcagtccctctgcagcagatgagcgtgactttggccatttcacgcactcgagtgtacacaatccatttttcttaaagcaaatgactgctgattgaccagatactgtaacgctgatttcgctccagatcgcacagatagcgaccatgttgctgcgtctgaaaatctggattccgaattcgaccctggcgctccatccatgcaacagatggcgacacttgttacaattcctgtcacccatcggcatggagcaggtccacttagattcccgatcacccacgcacatctcgctaatagtcattcgttcgtgtcttcgatcaatctcaagtgagtgtgcatggatcttggttgacgatgcggtatgggtttgcgccgctggctgcagggtctgcccaaggcaagctaacccagctcctctccccgacaatactctcgcaggcaaagccggtcacttgccttccagattgccaataaactcaattatggcctctgtcatgccatccatgggtctgatgaatggtcacgctcgtgtcctgaccgttccccagcctctggcgtcc

ggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctccT GATACAACTTAT tacgtaacggagcgtcgtgcgggagggagtgtgccgagcggggagtcccggtctgtgcgaggcccggcagctgacgctggcgagccgtacgccccgagggtccccctcccctgcaccctcttccccttccctctgacggccgcgcctgttct

catccactttctcggcgttcaatgcccgctgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcgctgccatcgccagcgaggtccccgtggccaccacctccccccgggcgcaccccaaggcgaacggcagcgcggtgtcgctgaagtcgggctccctggagacccaggaggacaagacgagcagctcgtccccccccccccgcacgttcatcaaccagctgcccgtgtggagcatgctgctgtcggcggtgaccacggtcttcggcgtggccgagaagcagtggcccatgctggaccgcaagtccaagcgccccgacatgctggtcgagcccctgggcgtggaccgcatcgtctacgacggcgtgagcttccgccagtcgttctccatccgcagctacgagatcggcgccgaccgcaccgcctcgatcgagacgctgatgaacatgttccaggagacctccctgaaccactgcaagatcatcggcctgctgaacgacggcttcggccgcacgcccgagatgtgcaagcgcgacctgatctgggtcgtgaccaagatgcagatcgaggtgaaccgctaccccacgtggggcgacaccatcgaggtcaacacgtgggtgagcgcctcgggcaagcacggcatgggccgcgactggctgatctccgactgccacaccggcgagatcctgatccgcgcgacgagcgtctgggcgatgatgaaccagaagacccgccgcctgtcgaagatcccctacgaggtgcgccaggagatcgagccccagttcgtcgactccgcccccgtgatcgtggacgaccgcaagttccacaagctggacctgaagacgggcgacagcatctgcaacggcctgaccccccgctggacggacctggacgtgaaccagcacgtcaacaacgtgaagtacatcggctggatcctgcagtcggtccccaccgaggtgttcgagacgcaggagctgtgcggcctgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagagcgtcacggccatggacccctcgaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgcggacatcgtgaagggccgcaccgagtggcgccccaagaacgccggcgccaagggcgccatcctgacgggcaagaccagcaacggcaactcgatctccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGA aagcttgcagcagcagctcgaagcttgcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctcccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaanctggagctccagcgccatgccacgccattgatggcttcaagtacgattacggtgttggattgtgtgtttgttgcgtagtgtgcatggtttagaataatacacttgatttcttgctcacggcaatctcggcttgtccgcaggttcaaccccatttcggagtctcaggtcagccgcgcaatgaccagccgctacttcaaggacttgcacgacaacgccgaggtgagctatgtttaggacttgattggaaattgtcgtcgacgcatattcgcgctccgcgacagcacccaagcaaaatgtcaagtgcgttccgatttgcgtccgcaggtcgatgttgtgatcgtcggcgccggatccgccggtctgtcctgcgcttacgagctgaccaagcaccctgacgtccgggtacgcgagctgagattcgattagacataaattgaagattaaacccgtagaaaaatttgatggtcgcgaaactgtgctcgattgcaagaaattgatcgtcctccactccgcaggtcgccatcatcgagcagggcgttgctcccggcggcggcgcctggctggggggacagctgttctcggccatgtgtgtacgtagaaggatgaatttcagctggttttcgttgcacagctgtttgtgcatgatttgtttcagactattgttgaatgtttttagatttcttaggatgcatgatttgtctgcatgcgactgaagagc 

Increased C12:0 levels in strain S5818 by the expression of heterologous“C14:0-specific” thioesterases. In an effort to increase C14:0 fattyacid levels in S5818, several thioesterases that had previouslydisplayed pronounced C14:0 thioesterase activity in P. moriformis weretransformed into the S5818 background. Contrary to our expectations, weobserved marked increases in C12:0 levels with decreases or onlymarginal increases in C14:0 levels. For example, introduction of theChsFATB3 thioesterase (which leads to an increase in C14:0 levels of upto 34% in S3150) into S5818 causes C12:0 levels to rise to ˜77% (Δ=+32%C12:0) and C14:0 levels to drop to ˜7% (Δ=−7%). In addition,introduction of CpalFATB2 into S5818 at the DAO1b locus causes C12:0levels to rise to ˜64% (Δ=+19%) and C14:0 levels to drop to ˜12%(Δ=−2%). The results for the top five transformants for each of the fiveconstructs are displayed in Table 83.

Of note, S5818 expresses the C. wrightii KASAI gene from the pLOOPlocus. As C. wrightii produces seed oil with 62% C12:0, we believe itlikely that the CwKASA1 gene has evolved to be specific for productionof C12:0 fatty acids when combined with C. wrightii thioesterases.Indeed, C. wrightii FATB2 encodes a thioesterase that exhibits C12:0activity when introduced into P. moriformis. Thus, it is possible thatthe “C14:0” thioesterase genes identified in our transcriptomesequencing, namely ChsFATB3 and ChtFATB1a, exhibit C14:0 activity onlywhen in combination with the P. moriformis endogenous KASI gene. Theseresults further extend to CpalFATB2, which has been repeatedly shown toincrease C14:0 levels in P. moriformis (data not shown). However, whenChsFATB3, ChtFATB1a, and CpalFATB2 are combined with a KASI gene from aCuphea species that produces high C12:0 fatty acids, such as CwKASA1from Cuphea wrightii, then a C12:0 activity of these thioesterases isrevealed/exhibited. It should be further noted that C. hyssopifolia andC. heterophylla produce only low levels of C14:0 in oilseeds (5% and 4%,respectively) while producing relatively high levels of C12:0 (84% and40%, respectively). Since the ChsFATB3 and ChtFATB1a thioesterases wereidentified from RNAs expressed in mature oil seeds, it is possible thatthese thioesterases indeed exhibited C12:0 activity in Cuphea seeds,significantly contributing to the high levels of C12:0 found therein.

Our results indicate that the combination of thioesterase and KAS islikely to be extremely important in determining the specificity of thethioesterase-KAS machinery in generating midchain fatty acids.Furthermore, introduction of heterologous KASs may be an important andfruitful approach for revealing novel specificities of additionalheterologous thioesterases.

TABLE 83 Fatty acid profiles for the top 5 transformants for each of thepSZ3493, pSZ3494, pSZ3495, pSZ3390, and pSZ3531 constructs uponintroduction into S5818. Sample ID pSZ#; construct Strain # C10:0 C12:0C14:0 C16:0 C18:0 C18:1 C18:2 N/A S5818 0.34 45.16 13.77 8.54 0.81 24.635.38 pSZ3493; ChsFATB3 Block 6; C6; pH 7; S5818; T678; D2202-30 0.7676.58 7.49 3.76 0.32 6.58 3.77 Block 6; D6; pH 7; S5818; T678; D2202-420.61 62.82 13.92 6.75 0.37 10.76 3.88 Block 6; D11; pH 7; S5818; T678;D2202-47 4.60 55.99 9.26 5.90 0.44 18.32 4.40 Block 6; A9; pH 7; S5818;T678; D2202-9 0.47 53.94 17.59 8.51 0.44 13.70 4.33 Block 6; D3; pH 7;S5818; T678; D2202-39 0.43 53.94 15.62 8.04 0.43 15.99 4.45 pSZ3494;Block 2; B8; pH 7; S5818; T678; D2203-20 0.43 56.76 14.15 7.60 0.5614.23 5.09 CpSAD1tp_trimmed: Block 2; C1; pH 7; S5818; T678; D2203-250.46 54.82 17.08 7.81 0.46 13.67 4.85 ChsFATB3 Block 2; D1; pH 7; S5818;T678; D2203-37 0.43 54.47 11.51 8.14 0.95 18.58 4.99 Block 2; D7; pH 7;S5818; T678; D2203-43 0.43 52.86 18.70 8.91 0.58 13.18 4.45 Block 2;C11; pH 7; S5818; T678; D2203-35 0.44 52.81 19.54 8.87 0.54 12.57 4.29pSZ3495; Block 2; G10; pH 7; S5818; T678; D2204-34 0.58 55.18 19.86 7.720.60 10.88 4.29 CpSAD1tp_trimmed: Block 2; H7; pH 7; S5818; T678;D2204-43 0.68 54.79 20.14 7.78 0.56 10.99 4.18 ChtFATB1a Block 2; H5; pH7; S5818; T678; D2204-41 0.60 54.69 20.38 7.39 0.55 11.50 4.13 Block 2;G8; pH 7; S5818; T678; D2204-32 0.66 54.26 20.39 7.69 0.55 11.45 4.26Block 2; F6; pH 7; S5818; T678; D2204-18 0.67 54.23 20.04 7.60 0.5611.80 4.23 pSZ3390; CpSAD1tpExt- Block 4; A5; pH 7; S5818; T674; D2104-50.58 63.83 12.10 5.89 0.55 10.46 5.44 CpalFATB2FLAGExtA Block 4; A12; pH7; S5818; T674; D2104-12 0.48 61.92 16.15 5.87 0.50 9.86 4.41 (DAO1b)Block 4; B9; pH 7; S5818; T674; D2104-21 0.41 54.31 18.41 7.26 0.5113.80 4.49 Block 4; B5; pH 7; S5818; T674; D2104-17 0.37 53.56 16.547.25 0.58 16.34 4.42 Block 4; B11; pH 7; S5818; T674; D2104-23 0.4152.44 17.99 7.60 0.54 15.38 4.66 pSZ3531; CpSAD1tpExt- Block 5B; A8; pH7; S5818; T684; D2235-8 0.52 59.36 15.70 6.93 0.45 11.41 4.63CpalFATB2FLAGExtA Block 5B; A12; pH 7; S5818; T684; D2235-12 0.44 55.6016.98 6.98 0.53 14.21 4.59 (THI4A) Block 5B; B11; pH 7; S5818; T684;D2235-23 0.36 49.58 17.43 8.72 0.57 17.44 4.62 Block 5B; A4; pH 7;S5818; T684; D2235-4 0.35 49.43 18.63 8.22 0.62 17.29 4.54 Block 5B;A11; pH 7; S5818; T684; D2235-11 0.36 48.92 15.93 7.84 0.68 20.38 4.96

Example 63 A Suite of Regulatable Promoters to Conditionally ControlGene Expression Levels in Oleaginous Cells in Synchrony with LipidProduction

S5204 was generated by knocking out both copies of FATA1 in Protothecamoriformis (PmFATA1) while simultaneously overexpressing the endogenousPmKASII gene in a Δfad2 line, S2532. S2532 itself is a FAD2 (also knownas FADc) double knockout strain that was previously generated byinsertion of C. tinctorius ACP thioesterase (Accession No: AAA33019.1)into S1331, under the control of CrTUB2 promoter at the FAD2 locus.S5204 and its parent S2532 have a disrupted endogenous PmFAD2-1 generesulting in no Δ12 specific desaturase activity manifested as 0% C18:2(linoleic acid) levels in both seed and lipid production stages. Lack ofany C18:2 in S5204 (and its parent S2532) results in growth defectswhich can be partially mitigated by exogenous addition of linoleic acidin the seed stage. For industrial applications of a zero linoleic oilhowever, exogenous addition of linoleic acid entails additional cost. Wehave previously shown that complementation of S5204 (and other Δfad2strains S2530 and S2532) with pH inducible AMT03p driven PmFAD2-1restores C18:2 to wild-type levels at pH 7.0 and also results in rescuedgrowth characteristics during seed stage without any linoleicsupplementation. Additionally when the seed from pH 7.0 growncomplemented lines is subsequently transferred into low-nitrogen lipidproduction flasks with pH adjusted to 5.0 (to control AMT03p driven FAD2protein levels), the resulting final oil profile matches the parentS5204 or S2532 profile with zero linoleic levels but with rescued growthand productivity metrics. Thus in essence with AMT03p driven FAD2-1 wehave developed a pH regulatable strain that potentially could be used togenerate oils with varying linoleic levels depending on the desiredapplication.

Prototheca moriformis undergoes rapid cell division during the first24-30 hrs in fermenters before nitrogen runs out in the media and thecells switch to storing lipids. This initial cell division and growth infermenters is critical for the overall strain productivity and, asreported above, FAD2 protein is crucial for sustaining vigorous growthcharacteristic of a particular strain. However when first generation,single insertion, genetically clean, PmFAD2-1 complemented strains(S4694 and S4695) were run in 7 L fermenters at pH 5.0 (with seed grownat pH 7.0), they did not perform on par with the original parent basestrain (S1331) in terms of productivity. Western data suggested thatAMT03p promoter driving PmFAD2-1 (as measured by FAD2 protein levels) isseverely down regulated between 0-30 hrs in fermenters irrespective offermenter pH (5.0 or 7.0). Work on fermentation conditions (batched vsunbatched/limited initial N, pH shift from 7 to 5 at different timepoints during production phase) suggested that initial batching (andexcess amounts) of nitrogen during early lipid production was the likelycause of AMT03p promoter down regulation in fermenters. Indeed, thisinitial repression in AMT03 can be directly seen in transcripttime-course during fermentation. A significant depression of Amt03expression was observed early in the run, which corresponds directlywith NH4 levels in the fermenter.

When the fermentations were performed with limited N, we were able topartially rescue the AMT03p promoter activity and while per cellproductivity of S4694/S4695 was on par with the parent S1331, theoverall productivity still lagged behind. These results suggest that asuboptimal or inactive AMT03p promoter and thus limitation of FAD2protein in early fermentation stages inhibits any complemented strainsfrom attaining their full growth potential and overall productivity.Here we identify new, improved promoter that allow differential geneactivity during high-nitrogen growth and low-nitrogen lipid productionphases.

In particular, we observed that:

-   -   In trans expression of the fatty acid desaturase-2 gene from        Prototheca moriformis (PmFad2-1) under the control of down        regulated promoter elements identified using a transcriptome        based bioinformatics approach results in functional        complementation of PmFAD2-1 with restored growth in Δfad2,        Δfata1 strain S5204.    -   Complementation of S5204 manifested in a robust growth phenotype        only occurs in seed and early fermentation stages when the new        promoter elements are actively driving the expression of        PmFAD2-1.    -   Once the cells enter the active lipid production phase (around        the time when N runs out in the fermenter), the newly identified        promoters are down regulated resulting in no additional FAD2        protein and the final oil profile of the complemented lines is        same as the parent S5204 albeit with better growth        characteristics.    -   These strains should potentially mitigate the problems that were        encountered with AMT03p driven FAD2 in earlier complemented        strains.    -   Importantly, we have identified down-regulatable promoters of        varying strengths, some of which are relatively strong in the        beginning with low-to-moderate levels provided during the        remainder of the run. Thus depending on phenotype these        promoters can be selected for fine-tuning the desired levels of        transgenes.

Bioinformatics Methods: RNA was prepared from cells taken from 8 timepoints during a typical fermenter run. RNA was polyA-selected for run onan Illumina HiSeq. Illumina paired-end data (100 bp reads×2, ˜600 bpfragment size) was collected and processed for read quality using FastQC[www.bioinformatics.babraham.ac.uk/projects/fastqc/]. Reads were runthrough a custom read-processing pipeline that de-duplicates,quality-trims, and length-trims reads.

Transcripts were assembled from Illumina paired-end reads usingOases/velvet [Velvet: algorithms for de novo short read assembly usingde Bruijn graphs. D. R. Zerbino and E. Birney. Genome Research18:821-829] and assessed by N50 and other metrics. The transcripts fromall 8 time points were further collapsed using CD-Hit. [Limin Fu,Beifang Niu, Zhengwei Zhu, Sitao Wu and Weizhong Li, CD-HIT: acceleratedfor clustering the next generation sequencing data. Bioinformatics,(2012), 28 (23): 3150-3152. doi: 10.1093/bioinformatics/bts565; Cd-hit:a fast program for clustering and comparing large sets of protein ornucleotide sequences”, Weizhong Li & Adam Godzik Bioinformatics, (2006)22:1658-9].

These transcripts were used as the base (reference assembly) forexpression-level analysis. Reads from the 8 time points were analyzedusing RSEM which provides raw read counts as well as a normalized valueprovided in Transcripts Per Million (TPM). [Li, Bo & Dewey, Colin N.(2011). RSEM: accurate transcript quantification from RNA-Seq data withor without a reference genome, BioMed Central: The Open AccessPublisher. Retrieved at Oct. 10, 2012, from the website temoa: OpenEducational Resources (OER) Portal at www.temoa.info/node/441614] TheTPM was used to determine expression levels. Genes previously identifiedin screens for strong promoters were also used to gauge which levelsshould be considered as significantly high or low. This data was loadedinto a Postgres database and visualized with Spotfire, along withintegrated data that includes gene function and other characteristicssuch as categorization based on expression profile. This enabled rapidand targeted analysis of genes with significant changes in expression.

The promoters for genes, which we selected, were mapped onto ahigh-quality reference genome for S376 (our reference Protothecamoriformis strain). Briefly, PacBio long reads (˜2 kb) wereerror-corrected by high-quality PacBio CCS reads (˜600 bp) and assembledusing the Allora assembler in SMRTPipe [pacbiodevnet.com]. Thisreference genome, in conjunction with transcriptome read mapping, wasused to annotate the precise gene structures, promoter and UTRlocations, and promoter elements within the region of interest, whichthen guided further sequencing and promoter element selection.

The criteria used for identifying new promoter elements were:

-   -   1. Reasonable expression (e.g., >500, <100, or <50 transcripts        per million [TPM]) of a downstream gene in seed and early lipid        production stages (T0-T30 hrs)    -   2. Severe down regulation of the gene above (e.g., >5-fold.        10-fold, or 15-fold) when the nitrogen gets depleted in the        fermenters.    -   3. pH neutrality of the promoter elements (e.g., less than a        2-fold change in TPM on going from pH 5.0 top 7.0 in cultivation        conditions), or at least effective operation under pH5        conditions.

Using the above described criteria we identified several potentiallydown regulated promoter elements that were eventually used to drivePmFAD2-1 expression in S5204. A range of promoters was chosen thatincluded some that started as being weak promoters and went down toextremely low levels, through those that started quite high and droppedonly to moderately low levels. This was done because it was unclear apriori how much expression would be needed for FAD2 early on to supportrobust growth, and how little FAD2 would be required during the lipidproduction phase in order to achieve the zero linoleic phenotype.

The promoter elements that were selected for screening and their allelicforms were named after their downstream gene and are as follows:

-   -   1. Carbamoyl phosphate synthase (PmCPS1p and PmCPS2p)    -   2. Dipthine synthase (PmDPS1p and PmDPS2p)    -   3. Inorganic pyrophosphatase (PmIPP1p)    -   4. Adenosylhomocysteinase (PmAHC1p and PmAHC2p)    -   5. Peptidyl-prolyl cis-trans isomerase (PmPPI1p and PmPPI2p)    -   6. GMP Synthetase (PmGMPS1p and PmGMPS2p)    -   7. Glutamate Synthase (PmGSp)    -   8. Citrate Synthase (PmCS1p and PmCS2p)    -   9. Gamma Glutamyl Hydrolase (PmGGH1p)    -   10. Acetohydroxyacid Isomerase (PmAHI1p and PmAHI2p)    -   11. Cysteine Endopeptidase (PmCEP1p)    -   12. Fatty acid desaturase 2 (PmFAD2-1p and PmFad2-2p) [CONTROL]

The transcript profile of two representative genes viz. PmIPP (InorganicPyrophosphatase) and PmAHC, (Adenosylhomocysteinase) start off verystrong (4000-5000 TPM) but once the cells enter active lipid productiontheir levels fall off very quickly. While the transcript levels of PmIPPdrop off to nearly 0 TPM, the levels of PmAHC drop to around 250 TPM andthen stay steady for the rest of the fermentation. All the otherpromoters (based on their downstream gene transcript levels) showedsimilar downward expression profiles.

The elements were PCR amplified and wherever possible promoters fromallelic genes were identified, cloned and named accordingly e.g. thepromoter elements for 2 genes of Carbamoyl phosphate synthase were namedPmCPS1p and PmCPS2p. As a comparator promoter elements from PmFAD2-1 andPmFAD2-2 were also amplified and used to drive PmFAD2-1 gene. While, inthe present example, we used FAD2-1 expression and hence C18:2 levels tointerrogate the newly identified down regulated promoters, in principlethese promoter elements can be used to down regulate any gene ofinterest.

Construct used for the expression of the Prototheca moriformis fattyacid desaturase 2 (PmFAD2-1) under the expression of PmCPS1p in dfad2strains S5204—[pSZ3377]: The Δfad2 Δfata1 S5204 strain was transformedwith the construct pSZ3377. The sequence of the transforming DNA isprovided below. Relevant restriction sites in the construct pSZ3377(6S::PmHXT1p-ScMEL1-CvNR::PmCPS1p-PmFAD2-1-CvNR::6S) are indicated inlowercase, underlined and bold, and are from 5′-3′ BspQ 1, KpnI, SpeI,SnaBI, EcoRV, SpeI, AflII, SacI, BspQ I, respectively. BspQI sitesdelimit the 5′ and 3′ ends of the transforming DNA. Bold, lowercasesequences represent genomic DNA from UTEX 1435 that permits targetedintegration of the transforming DNA at the 6S locus via homologousrecombination. Proceeding in the 5′ to 3′ direction, the Hexosetransporter (HXT1) gene promoter from UTEX 1435 driving the expressionof the Saccharomyces cerevisiae Melibiase (ScMEL1) gene is indicated bythe boxed text. The initiator ATG and terminator TGA for ScMEL1 areindicated by uppercase, bold italics while the coding region isindicated in lowercase italics. The Chlorella vulgaris nitrate reductase3′ UTR is indicated by lowercase underlined text followed by an UTEX1435 CPS1p promoter of Prototheca moriformis, indicated by boxed italicstext. The Initiator ATG and terminator TGA codons of the PmFAD2-1 areindicated by uppercase, bold italics, while the remainder of the gene isindicated by bold italics. The C. vulgaris nitrate reductase 3′ UTR isagain indicated by lowercase underlined text followed by the UTEX 14356S genomic region indicated by bold, lowercase text. The final constructwas sequenced to ensure correct reading frames and targeting sequences.

Nucleotide sequence of transforming DNA contained in plasmid pSZ3377:(SEQ ID NO: 128) gctcttcggagtcactgtgccactgagttcgactggtagctgaatggagtcgctgctccactaaacgaattgtcagcaccgccagccggccgaggacccgagtcatagcgagggtagtagcgcgccatggcaccgaccagcctgcttgccagtactggcgtctcttccgcttctctgtggtcctctgcgcgctccagcgcgtgcgcttttccggtggatcatgcggtccgtggcgcaccgcagcggccgctgcccatgcagcgccgctgcttccgaacagtggcggtcagggccgcacccgcggtagccgtccgtccggaacccgcccaagagttttgggagcagcttgagccctgcaagatggcggaggacaagcgcatcttcctggaggagcaccggtgcgtggaggtccggggctgaccggccgtcgcattcaacgtaatcaatcgcatgatgatcagaggacacgaagtcttggtggcggtggccagaaacactgtccattgcaagggcatagggatgcgttccttcacctctcatttctcatttctgaatccctccctgctcactctttctcctcctccttc

gcctgcatctccctgaagggcgtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaagtacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctactcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctccTGAtacgtagcagcagcagtcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaat

cagcccgtggagaagccccccttcaccatcggcaccctgcgcaaggccatccccgcccactgcttcgagcgctccgccctgcgctcctccatgtacctggccttcgacatcgccgtgatgtccctgctgtacgtggcctccacctacatcgaccccgcccccgtgcccacctgggtgaagtacggcgtgatgtggcccctgtactggttcttccagggcgccttcggcaccggcgtgtgggtgtgcgcccacgagtgcggccaccaggccttctcctcctcccaggccatcaacgacggcgtgggcctggtgttccactccctgctgctggtgccctactactcctggaagcactcccaccgccgccaccactccaacaccggctgcctggacaaggacgaggtgttcgtgcccccccaccgcgccgtggcccacgagggcctggagtgggaggagtggctgcccatccgcatgggcaaggtgctggtgaccctgaccctgggctggcccctgtacctgatgttcaacgtggcctcccgcccctacccccgcttcgccaaccacttcgacccctggtcccccatcttctccaagcgcgagcgcatcgaggtggtgatctccgacctggccctggtggccgtgctgtccggcctgtccgtgctgggccgcaccatgggctgggcctggctggtgaagacctacgtggtgccctacctgatcgtgaacatgtggctggtgctgatcaccctgctgcagcacacccaccccgccctgccccactacttcgagaaggactgggactggctgcgcggcgccatggccaccgtggaccgctccatgggcccccccttcatggacaacatcctgcaccacatctccgacacccacgtgctgcaccacctgttctccaccatcccccactaccacgccgaggaggcctccgccgccatccgccccatcctgggcaagtactaccagtccgactcccgctgggtgggccgcgccctgtgggaggactggcgcgactgccgctacgtggtgcccgacgcccccgaggacgactccgccctgtggttccacaagTAGatcgatcttaaggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatcccatccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaaagcttaattaa gagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaatttaaaagcttggaatgttggttcgtgcgtctggaacaagcccagacttgttgctcactgggaaaaggaccatcagctccaaaaaacttgccgctcaaaccgcgtacctctgctttcgcgcaatctgccctgttgaaatcgccaccacattcatattgtgacgcttgagcagtctgtaattgcctcagaatgtggaatcatctgccccctgtgcgagcccatgccaggcatgtcgcgggcgaggacacccgccactcgtacagcagaccattatgctacctcacaatagttcataacagtgaccatatttctcgaagctccccaacgagcacctccatgctctgagtggccaccccccggccctggtgcttgcggagggcaggtcaaccggcatggggctaccgaaatccccgaccggatcccaccacccccgcgatgggaagaatctctccccgggatgtgggcccaccaccagcacaacctgctggcccaggcgagcgtcaaaccataccacacaaatatccttggcatcggccctgaattccttctgccgctctgctacccggtgcttctgtccgaagcaggggttgctagggatcgctccgagtccgcaaacccttgtcgcgtggcggggcttgttcgagctt gaagagc  

The recombination between C. vulgaris nitrate reductase 3′ UTR's in theconstruct pSZ3377 results in multiple copies of PmFAD2-1 in transgeniclines which would then manifest most likely as higher C18:2 levels atthe end of fermentation. Since the goal was to create a strain with 0%terminal C18:2, we took precautions to avoid this recombination. Inanother version of the above plasmid ScMEL1 gene was followed byChlorella protothecoides (UTEX 250) elongation factor 1a (CpEF1a) 3′ UTRinstead of C. vulgaris 3′ UTR. The sequence of C. protothecoides (UTEX250) elongation factor 1a (CpEF1a) 3′ UTR used in construct pSZ3384 andother constructs with this 3′ UTR (described below) is shown below.Plasmid pSZ3384 could be written as6S::PmHXT1p-ScMEL1-CpEF1a::PmCPS1p-PmFAD2-1-CvNR::6S.

Nucleotide sequence of Chlorella protothecoides (UTEX 250) elongationfactor 1a (CpEF1a) 3′ UTR in pSZ3384:

(SEQ ID NO: 129) tacaacttat tacgta acggagcgtcgtgcgggagggagtgtgccgagcggggagtcccggtctgtgcgaggcccggcagctgacgctggcgagccgtacgccccgagggtccccctcccctgcaccctcttccccttccctctgacggccgcgcctgttcttgcatgttcagcgacgag gatatc

The C. protothecoides (UTEX 250) elongation factor 1a 3′ UTR sequence isflanked by restriction sites SnaBI on 5′ and EcoRV on 3′ ends shown inlowercase bold underlined text. Note that the plasmids containing CpEF1a3′ UTR (pSZ3384 and others described below) after ScMEL1 stop codoncontains 10 extra nucleotides before the 5′ SnaBI site. Thesenucleotides are not present in the plasmids that contain C. vulgarisnitrate reductase 3′ UTR after the S. ScMEL1 stop codon.

In addition to plasmids pSZ3377 and pSZ3384 expressing either arecombinative CvNR-Promoter-PmFAD2-1-CvNR or non-recombinativeCpEF1a-Promoter-PmFAD2-1-CvNR expression unit described above, plasmidsusing other promoter elements mentioned above were constructed forexpression in S5204. These constructs along with their transformationidentifiers (D #) can be described as:

Plasmid ID D # Description pSZ3378 D20906SA::pPmHXT1-ScarIMEL1-CvNR:PmCPS2p-PmFad2-1-CvNR::6SB pSZ3385 D20976SA::pPmHXT1-ScarIMEL1-CpEF1a:PmCPS2p-PmFad2-1-CvNR::6SB pSZ3379 D20916SA::pPmHXT1-ScarIMEL1-CvNR:PmDPS1p-PmFad2-1-CvNR::6SB pSZ3386 D20986SA::pPmHXT1)-ScarIMEL1-CpEF1a:PmDPS1p-PmFad2-1-CvNR::6SB pSZ3380 D20926SA::pPmHXT1-ScarIMEL1-CvNR:PmDPS2p-PmFad2-1-CvNR::6SB pSZ3387 D20996SA::pPmHXT1-ScarIMEL1-CpEF1a:PmDPS2p-PmFad2-1-CvNR::6SB pSZ3480 D22596SA::pPmHXT1-ScarIMEL1-CvNR:PmIPP1p-PmFad2-1-CvNR::6SB pSZ3481 D22606SA::pPmHXT1-ScarIMEL1-CpEF1a:PmIPP1p-PmFad2-1-CvNR::6SB pSZ3509 D24346SA::pPmHXT1-ScarIMEL1-CvNR:PmAHC1p-PmFad2-1-CvNR::6SB pSZ3516 D22666SA::pPmHXT1-ScarIMEL1-CpEF1a:PmAHC1p-PmFad2-1-CvNR::6SB pSZ3510 D24356SA::pPmHXT1-ScarIMEL1-CvNR:PmAHC2p-PmFad2-1-CvNR::6SB pSZ3513 D22636SA::pPmHXT1-ScarIMEL1-CvNR:PmPPI1p-PmFad2-1-CvNR::6SB pSZ3689 D24406SA::pPmHXT1-ScarIMEL1-CpEF1a:PmPPI1p-PmFad2-1-CvNR::6SB pSZ3514 D22646SA::pPmHXT1-ScarIMEL1-CvNR:PmPPI2p-PmFad2-1-CvNR::6SB pSZ3518 D22686SA::pPmHXT1-ScarIMEL1-CpEF1a:PmPPI2p-PmFad2-1-CvNR::6SB pSZ3515 D22656SA::pPmHXT1-ScarIMEL1-CvNR:PmGMPS1p-PmFad2-1-CvNR::6SB pSZ3519 D22696SA::pPmHXT1-ScarIMEL1-CpEF1a:PmGMPS1p-PmFad2-1-CvNR::6SB pSZ3520 D22706SA::pPmHXT1-ScarIMEL1-CpEF1a:PmGMPS2p-PmFad2-1-CvNR::6SB pSZ3684 D24366SA::pPmHXT1-ScarIMEL1-CvNR:PmCS1p-PmFad2-1-CvNR::6SB pSZ3686 D24386SA::pPmHXT1-ScarIMEL1-CpEF1A:PmCS1p-PmFad2-1-CvNR::6SB pSZ3685 D24376SA::pPmHXT1-ScarIMEL1-CvNR:PmCS2p-PmFad2-1-CvNR::6SB pSZ3688 D24396SA::pPmHXT1-ScarIMEL1-CvNR:PmGGHp-PmFad2-1-CvNR::6SB pSZ3511 D22616SA::pPmHXT1-ScarIMEL1-CvNR:PmAHI2p-PmFad2-1-CvNR::6SB pSZ3517 D22676SA::pPmHXT1-ScarIMEL1-CpEF1a:PmAHI1p-PmFad2-1-CvNR::6SB pSZ3512 D22626SA::pPmHXT1-ScarIMEL1-CvNR:PmCEP1p-PmFad2-1-CvNR::6SB pSZ3375 D20876SA::pPmHXT1-ScarIMEL1-CvNR:PmFAD2-1p-PmFad2-1-CvNR::6SB pSZ3382 D20946SA::pPmHXT1-ScarIMEL1-CpEF1a:PmFAD2-1p-PmFad2-1-CvNR::6SB pSZ3376 D20886SA::pPmHXT1-ScarIMEL1-CvNR:PmFAD2-2p-PmFad2-1-CvNR::6SB pSZ3383 D20956SA::pPmHXT1-ScarIMEL1-CpEF1a:PmFAD2-2p-PmFad2-1-CvNR::6SB

The above constructs are the same as pSZ3377 or pSZ3384 except for thepromoter element that drives PmFAD2-1. The sequences of differentpromoter elements used in the above constructs are shown below.

Nucleotide sequence of Carbamoyl phosphate synthase allele 2 promoter containedin plasmid pSZ3378 and pSZ3385 (PmCPS2p promoter sequence):(SEQ ID NO: 130)

Nucleotide sequence of Dipthine synthase allele 1 promoter contained in plasmidpSZ3379 and pSZ3386 (PmDPS1p promoter sequence): (SEQ ID NO: 131)

Nucleotide sequence of Dipthine synthase allele 2 promoter contained in plasmidpSZ3380 and pSZ3387 (PmDPS2p promoter sequence): (SEQ ID NO: 132)

Nucleotide sequence of Inorganic pyrophosphatase allele 1 promoter contained inplasmid pSZ3480 and pSZ3481 (PmIPP1p promoter sequence): (SEQ ID NO:133)

Nucleotide sequence of Adenosylhomocysteinase allele 1 promoter contained inplasmid pSZ3509 and pSZ3516 (PmAHC1p promoter sequence):(SEQ ID NO: 134)

Nucleotide sequence of Adenosylhomocysteinase allele 2 promoter contained inplasmid pSZ3510 (PmAHC2p promoter sequence): (SEQ ID NO: 135)

Nucleotide sequence of Peptidyl-prolyl cis-trans isomerase allele 1 promotercontained in plasmid pSZ3513 and pSZ3689 (PmPPI1p promoter sequence):(SEQ ID NO: 136)

Nucleotide sequence of Peptidyl-prolyl cis-trans isomerase allele 2 promotercontained in plasmid pSZ3514 and pSZ3518 (PmPPI2p promoter sequence):(SEQ ID NO: 137)

Nucleotide sequence of GMP Synthetase allele 1 promoter contained in plasmidpSZ3515 and pSZ3519 (PmGMPS1p promoter sequence): (SEQ ID NO: 138)

Nucleotide sequence of GMP Synthetase allele 2 promoter contained in plasmidpSZ3520 (PmGMPS2p promoter sequence): (SEQ ID NO: 139)

Nucleotide sequence of Citrate synthase allele 1 promoter contained in plasmidpSZ3684 and pSZ3686 (PmCS1p promoter sequence): (SEQ ID NO: 140)

Nucleotide sequence of Citrate synthase allele 2 promoter contained in plasmidpSZ3685 (PmCS2p promoter sequence): (SEQ ID NO: 141)

Nucleotide sequence of Gamma Glutamyl Hydrolase allele 1 promoter contained inplasmid pSZ3688 (PmGGH1p promoter sequence): (SEQ ID NO: 142)

Nucleotide sequence of Acetohydroxyacid Isomerase allele 1 promoter contained inplasmid pSZ3517 (PmAHI1p promoter sequence): (SEQ ID NO: 143)

Nucleotide sequence of Acetohydroxyacid Isomerase allele 2 promoter contained inplasmid pSZ3511 (PmAHI2p promoter sequence): (SEQ ID NO: 144)

Nucleotide sequence of Cysteine Endopeptidase allele 1 promoter contained inplasmid pSZ3512 (PmCEP1 promoter sequence): (SEQ ID NO: 145)

Nucleotide sequence of Fatty acid desaturase 2 allele 1 promoter contained inplasmid pSZ3375 and 3382 (PmFAD2-1 promoter sequence): (SEQ ID NO: 146)

Nucleotide sequence of Fatty acid desaturase 2 allele 2 promoter contained inplasmid pSZ3376 and 3383 (PmFAD2-2 promoter sequence): (SEQ ID NO: 147)

To determine their impact on growth and fatty acid profiles, theabove-described constructs were independently transformed into a Δfad2Δfata1 strain S5204. Primary transformants were clonally purified andgrown under standard lipid production conditions at pH5.0 or at pH7.0.The resulting profiles from a set of representative clones arising fromtransformations are shown in Tables 84-114.

TABLE 84 Fatty acid profile in some representative complemented (D2087)and parent S5204 lines transformed with pSZ3375 DNA containing PmFAD2-1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH 7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH 5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH 7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH 5; S5204 0.39 5.671.36 91.13 0 0 pH 7; S5204; T665; D2087-22 0.38 4.43 1.78 83.93 7.580.81 pH 7; S5204; T665; D2087-16 0.41 4.92 1.94 83.21 7.55 0.84 pH 7;S5204; T665; D2087-17 0.40 4.82 1.78 83.51 7.52 0.79 pH 7; S5204; T665;D2087-26 1.30 8.06 2.54 79.03 7.30 0.82 pH 7; S5204; T665; D2087-29 1.137.88 2.45 79.48 7.26 0.79

TABLE 85 Fatty acid profile in some representative complemented (D) andparent S5204 lines transformed with pSZ3382 DNA containing PmFAD2-1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH 7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH 5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH 7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH 5; S5204 0.39 5.671.36 91.13 0 0 pH 7; S5204; T672; D2094-5 0.49 5.76 2.95 83.39 5.08 0.84pH 7; S5204; T672; D2094-25 0.35 5.01 2.41 85.10 5.09 0.64 pH 7; S5204;T672; D2094-13 0.33 5.07 2.30 84.89 5.30 0.69 pH 7; S5204; T672;D2094-11 0.38 4.33 1.78 85.63 5.31 0.85 pH 7; S5204; T672; D2094-8 0.355.29 2.32 84.59 5.34 0.66

TABLE 86 Fatty acid profile in some representative complemented (D2088)and parent S5204 lines transformed with pSZ3376 DNA containing PmFAD2-2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH 7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH 5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH 7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH 5; S5204 0.39 5.671.36 91.13 0 0 pH 7; S5204; T665; D2088-16 1.11 8.18 2.92 78.13 6.960.87 pH 7; S5204; T665; D2088-20 1.06 7.78 2.95 78.65 6.95 0.84 pH 7;S5204; T665; D2088-29 0.91 7.13 2.87 79.63 6.93 0.78 pH 7; S5204; T665;D2088-6 1.18 8.29 2.98 77.90 6.91 0.88 pH 7; S5204; T665; D2088-18 1.107.98 3.09 78.42 6.78 0.81

TABLE 87 Fatty acid profile in some representative complemented (D) andparent S5204 lines transformed with pSZ3383 DNA containing PmFAD2-2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH7; S5204; T673; 0.30 5.43 2.45 85.10 4.62 0.68 D2095-47pH7; S5204; T673; 0.38 5.16 2.48 84.46 5.41 0.68 D2095-14 pH7; S5204;T673; 0.43 4.60 2.54 84.82 5.47 0.58 D2095-16 pH7; S5204; T673; 0.345.41 2.57 84.21 5.49 0.66 D2095-6 pH7; S5204; T673; 0.42 5.30 2.49 83.975.57 0.68 D2095-39

TABLE 88 Fatty acid profile in representative complemented (D2089) andparent S5204 lines transformed with pSZ3377 DNA containing PmCPS1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T672; 0.35 4.73 2.29 88.94 1.79 0.39D2089-40 pH7; S5204; T672; 0.51 4.85 2.96 87.55 2.05 0.41 D2089-2 pH7;S5204; T672; 0.56 5.00 3.04 87.24 2.07 0.36 D2089-14 pH7; S5204; T672;0.38 5.04 2.39 88.02 2.39 0.44 D2089-7 pH7; S5204; T672; 0.38 5.00 2.3787.93 2.42 0.43 D2089-18

TABLE 89 Fatty acid profile in some representative complemented (D2096)and parent S5204 lines transformed with pSZ3384 DNA containing PmCPS1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T673; 0.33 4.18 1.10 92.91 0.00 0.00D2096-6 pH7; S5204; T673; 0.36 4.14 1.33 92.42 0.34 0.12 D2096-12 pH7;S5204; T673; 0.32 4.35 1.64 92.12 0.35 0.14 D2096-14 pH7; S5204; T673;0.50 6.44 0.95 89.81 0.46 0.32 D2096-8 pH7; S5204; T673; 0.29 3.93 1.7991.19 1.34 0.37 D2096-1

TABLE 90 Fatty acid profile in some representative complemented (D2090)and parent S5204 lines transformed with pSZ3378 DNA containing PmCPS2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T672; 0.33 4.73 1.84 91.24 0.00 0.00D2090-5 pH7; S5204; T672; 0.42 4.99 2.01 91.06 0.00 0.00 D2090-29 pH7;S5204; T672; 0.43 4.31 1.87 90.44 0.78 0.16 D2090-22 pH7; S5204; T672;0.32 3.77 2.43 89.72 1.68 0.35 D2090-1 pH7; S5204; T672; 0.49 5.01 1.9788.48 1.84 0.38 D2090-32

TABLE 91 Fatty acid profile in some representative complemented (D2097)and parent S5204 lines transformed with pSZ3385 DNA containing PmCPS2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH5; S5204; T680; 0.50 5.73 1.97 87.12 2.61 0.76D2097-1 pH5; S5204; T680; 0.75 8.20 2.46 85.73 0.89 0.53 D2097-2

TABLE 92 Fatty acid profile in some representative complemented (D2091)and parent S5204 lines transformed with pSZ3379 DNA containing PmDPS1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T672; 1.42 4.39 2.32 89.87 0.00 0.00D2091-4 pH7; S5204; T672; 0.27 4.79 2.24 90.94 0.00 0.00 D2091-14 pH7;S5204; T672; 0.30 5.26 2.20 90.73 0.00 0.00 D2091-15 pH7; S5204; T672;0.31 4.51 1.77 91.65 0.00 0.00 D2091-19 pH7; S5204; T672; 0.31 5.36 2.2490.67 0.00 0.00 D2091-46

TABLE 93 Fatty acid profile in some representative complemented (D2098)and parent S5204 lines transformed with pSZ3386 DNA containing PmDPS1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T680; 0.34 4.89 1.56 92.08 0.00 0.00D2098-39 pH7; S5204; T680; 0.30 4.31 1.61 92.34 0.30 0.00 D2098-7 pH7;S5204; T680; 0.33 3.89 1.58 92.65 0.36 0.00 D2098-3 pH7; S5204; T680;0.32 4.18 1.64 92.34 0.36 0.11 D2098-25 pH7; S5204; T680; 0.32 4.36 1.5092.10 0.37 0.12 D2098-13

TABLE 94 Fatty acid profile in some representative complemented (D2092)and parent S5204 lines transformed with pSZ3380 DNA containing PmDPS2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T672; 0.29 5.13 1.59 92.16 0.00 0.00D2092-35 pH7; S5204; T672; 0.37 4.66 1.75 91.71 0.19 0.05 D2092-29 pH7;S5204; T672; 0.24 3.47 1.84 93.19 0.43 0.11 D2092-15 pH7; S5204; T672;0.25 3.50 1.82 93.16 0.44 0.09 D2092-21 pH7; S5204; T672; 0.28 3.18 1.5093.59 0.52 0.12 D2092-16

TABLE 95 Fatty acid profile in some representative complemented (D2099)and parent S5204 lines transformed with pSZ3387 DNA containing PmDPS2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH7; S5204; T680; 0.31 4.02 1.46 93.07 0.00 0.00D2099-20 pH7; S5204; T680; 0.28 4.67 1.50 92.38 0.00 0.00 D2099-24 pH7;S5204; T680; 0.40 4.07 1.22 93.26 0.00 0.00 D2099-27 pH7; S5204; T680;0.32 4.59 1.57 92.40 0.00 0.00 D2099-30 pH7; S5204; T680; 0.30 4.56 1.5492.49 0.00 0.00 D2099-35

TABLE 96 Fatty acid profile in some representative complemented (D2259)and parent S5204 lines transformed with pSZ3480 DNA containing PmIPP1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH5; S5204; T711; 0.36 5.27 2.19 89.32 1.51 0.51D2259-43 pH5; S5204; T711; 0.35 4.88 2.17 86.34 4.41 0.70 D2259-22 pH5;S5204; T711; 0.35 4.82 2.18 86.32 4.45 0.69 D2259-28 pH5; S5204; T711;0.33 4.90 2.08 86.33 4.49 0.74 D2259-21 pH5; S5204; T711; 0.50 5.97 2.1484.67 4.49 0.74 D2259-36

TABLE 97 Fatty acid profile in some representative complemented (D2260)and parent S5204 lines transformed with pSZ3481 DNA containing PmIPP1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.10 0.00 pH5; S5204 0.39 5.671.36 91.13 0.00 0.00 pH5; S5204; T711; 0.36 4.96 2.10 89.46 1.55 0.49D2260-32 pH5; S5204; T711; 0.33 4.83 1.99 89.40 1.63 0.58 D2260-10 pH5;S5204; T711; 0.34 4.83 2.16 89.39 1.64 0.49 D2260-2 pH5; S5204; T711;0.37 4.81 2.11 89.51 1.69 0.26 D2260-30 pH5; S5204; T711; 0.33 4.91 2.1789.73 1.72 0.16 D2260-41

TABLE 98 Fatty acid profile in some representative complemented (D2434)and parent S5204 lines transformed with pSZ3509 DNA containing PmAHC1pdriving PmFAD2-1. Sample ID C14.0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.33 4.45 1.55 81.55 8.51 1.38 T768; D2434-32pH5; S5204; 0.62 7.27 1.58 78.65 9.44 1.49 T768; D2434-27 pH5; S5204;0.38 5.81 1.79 79.63 10.01 1.18 T768; D2434-4 pH5; S5204; 0.5 5.93 1.578.7 10.25 1.56 T768; D2434-23 pH5; S5204; 0.51 6.08 1.6 78.79 10.251.36 T768; D2434-43

TABLE 99 Fatty acid profile in some representative complemented (D2266)and parent S5204 lines transformed with pSZ3516 DNA containing PmAHC1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; T718; 0.32 5.41 1.94 91.26 0.11 0.00 D2266-46pH5; S5204; T718; 0.36 5.33 1.90 91.17 0.17 0.00 D2266-36 pH5; S5204;T718; 0.37 4.96 2.13 90.82 0.41 0.00 D2266-35 pH5; S5204; T718; 0.385.33 2.10 90.31 0.44 0.31 D2266-41 pH5; S5204; T718; 0.36 5.15 2.2390.55 0.48 0.31 D2266-5

TABLE 100 Fatty acid profile in some representative complemented (D2435)and parent S5204 lines transformed with pSZ3510 DNA containing PmAHC2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; T768; 0.35 6.09 1.90 78.52 11.01 1.18D2435-37 pH5; S5204; T768; 0.43 5.90 1.97 78.74 10.97 1.20 D2435-3 pH5;S5204; T768; 0.40 6.01 1.89 79.00 10.97 1.14 D2435-20 pH5; S5204; T768;0.39 6.11 1.89 78.26 10.84 1.24 D2435-13 pH5; S5204; T768; 0.46 6.021.97 79.48 10.46 1.19 D2435-34

TABLE 101 Fatty acid profile in some representative complemented (D2263)and parent S5204 lines transformed with pSZ3513 DNA containing PmPPI1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; T718; 0.75 9.44 1.98 87.09 0.00 0.00 D2263-13pH5; S5204; T718; 0.58 7.72 1.64 89.26 0.00 0.00 D2263-14 pH5; S5204;T718; 0.62 7.92 1.56 89.25 0.00 0.00 D2263-19 pH5; S5204; T718; 0.427.39 1.70 89.28 0.00 0.00 D2263-26 pH5; S5204; T718; 0.58 7.32 1.3090.07 0.00 0.00 D2263-29

TABLE 102 Fatty acid profile in some representative complemented (D2440)and parent S5204 lines transformed with pSZ3689 DNA containing PmPPI1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.31 6.24 1.41 90.42 0.17 0.05 T770; D2440-23pH5; S5204; 0.23 4.69 1.41 91.72 0.17 0.00 T770; D2440-32 pH5; S5204;0.30 6.31 1.49 90.21 0.17 0.00 T770; D2440-38 pH5; S5204; 0.30 6.33 1.3890.29 0.18 0.05 T770; D2440-7 pH5; S5204; 0.29 6.38 1.36 90.39 0.18 0.05T770; D2440-36 pH5; S5204; 0.34 5.63 1.15 91.15 0.19 0.05 T770; D2440-8

TABLE 103 Fatty acid profile in some representative complemented (D2264)and parent S5204 lines transformed with pSZ3514 DNA containing PmPPI2pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH7; S6207; 0.49 6.15 1.61 90.82 0.00 0.00 T718; D2264-1pH7; S6207; 0.38 5.36 1.51 91.58 0.00 0.00 T718; D2264-6 pH7; S6207;0.45 6.09 1.46 91.10 0.00 0.00 T718; D2264-29 pH7; S6207; 0.40 5.42 2.2889.86 0.90 0.00 T718; D2264-4 pH7; S6207; 0.40 5.37 2.02 90.18 1.04 0.00T718; D2264-7

TABLE 104 Fatty acid profile in some representative complemented (D2268)and parent S5204 lines transformed with pSZ3518 DNA containing PmPPI2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.39 6.43 1.78 90.49 0.00 0.00 T720; D2268-1pH5; S5204; 0.38 6.49 1.74 90.38 0.00 0.00 T720; D2268-2 pH5; S5204;0.38 6.56 1.74 90.27 0.00 0.00 T720; D2268-3 pH5; S5204; 0.45 5.73 1.5291.75 0.00 0.00 T720; D2268-4 pH5; S5204; 0.38 6.58 1.81 90.79 0.00 0.00T720; D2268-5

TABLE 105 Fatty acid profile in some representative complemented (D2265)and parent S5204 lines transformed with pSZ3515 DNA containing PmGMPS1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.46 7.02 1.71 90.06 0.00 0.00 T718; D2265-16pH5; S5204; 0.00 7.90 1.90 89.27 0.00 0.00 T718; D2265-43 pH5; S5204;0.46 5.53 1.68 91.28 0.35 0.00 T718; D2265-14 pH5; S5204; 0.39 6.17 1.7590.44 0.42 0.00 T718; D2265-4 pH5; S5204; 0.49 5.87 1.77 90.51 0.45 0.00T718; D2265-9

TABLE 106 Fatty acid profile in some representative complemented (D2269)and parent S5204 lines transformed with pSZ3519 DNA containing PmGMPS1pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.38 6.73 1.68 90.24 0.00 0.00 T720; D2269-1pH5; S5204; 0.36 6.76 1.71 90.17 0.00 0.00 T720; D2269-3 pH5; S5204;0.42 6.57 1.71 90.32 0.00 0.00 T720; D2269-4 pH5; S5204; 0.59 8.81 1.9387.97 0.00 0.00 T720; D2269-5 pH5; S5204; 0.50 7.29 1.73 89.29 0.00 0.00T720; D2269-6

TABLE 107 Fatty acid profile in some representative complemented (D2270)and parent S5204 lines transformed with pSZ3520 DNA containing PmGMPS2pdriving PmFAD2-1. Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 C18:3 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.37 6.80 1.74 90.18 0.00 0.00 T720; D2270-1pH5; S5204; 0.46 6.76 1.83 89.90 0.00 0.00 T720; D2270-2 pH5; S5204;0.41 6.69 1.70 90.22 0.00 0.00 T720; D2270-3 pH5; S5204; 0.43 7.44 1.7289.31 0.00 0.00 T720; D2270-4 pH5; S5204; 0.44 6.98 1.78 89.79 0.00 0.00T720; D2270-5

TABLE 108 Fatty acid profile in some representative complemented (D2436)and parent S5204 lines transformed with pSZ3684 DNA containing PmCS1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 7.59 1.57 88.88 0.18 0.00 0.00 T768; D2436-48pH5; S5204; 6.37 1.50 85.00 3.97 1.04 0.00 T768; D2436-1 pH5; S5204;9.40 1.86 81.13 4.11 1.21 0.00 T768; D2436-16 pH5; S5204; 6.07 1.7784.78 4.26 0.94 0.00 T768; D2436-8 pH5; S5204; 5.97 1.62 85.28 4.50 0.980.00 T768; D2436-32

TABLE 109 Fatty acid profile in some representative complemented (D2438)and parent S5204 lines transformed with pSZ3686 DNA containing PmCS1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.50 5.96 1.69 89.87 1.30 0.00 T770; D2438-7pH5; S5204; 0.41 6.05 1.86 87.88 2.46 0.00 T770; D2438-11 pH5; S5204;0.41 5.75 1.93 88.35 2.50 0.00 T770; D2438-9 pH5; S5204; 0.45 6.18 1.8587.86 2.59 0.00 T770; D2438-15 pH5; S5204; 0.40 5.92 1.97 87.80 2.590.00 T770; D2438-37

TABLE 110 Fatty acid profile in some representative complemented (D2437)and parent S5204 lines transformed with pSZ3685 DNA containing PmCSCpdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.00 4.83 1.98 90.43 1.17 0.53 T768; D2437-15pH5; S5204; 0.45 6.03 1.81 88.69 1.88 0.31 T768; D2437-35 pH5; S5204;0.39 4.96 2.00 88.58 3.24 0.00 T768; D2437-17 pH5; S5204; 0.90 9.55 2.0782.29 3.37 1.24 T768; D2437-26 pH5; S5204; 0.53 10.76 1.55 79.62 4.461.12 T768; D2437-8

TABLE 111 Fatty acid profile in some representative complemented (D2439)and parent S5204 lines transformed with pSZ3688 DNA containing PmGGHpdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.31 6.79 1.47 89.97 0.00 0.00 T770; D2439-11pH5; S5204; 0.27 4.19 0.94 92.91 0.08 0.00 T770; D2439-22 pH5; S5204;0.39 6.02 1.26 90.91 0.16 0.00 T770; D2439-12 pH5; S5204; 0.64 6.50 1.1089.53 0.20 0.00 T770; D2439-34 pH5; S5204; 0.33 5.25 1.45 89.98 1.080.51 T770; D2439-32

TABLE 112 Fatty acid profile in some representative complemented (D2261)and parent S5204 lines transformed with pSZ3511 DNA containing PmAHI2pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.45 5.06 2.02 89.35 1.73 0.63 T711; D2261-35pH5; S5204; 0.46 5.12 2.19 88.92 2.16 0.19 T711; D2261-8 pH5; S5204;0.37 5.12 2.15 88.62 2.30 0.45 T711; D2261-43 pH5; S5204; 0.42 5.27 2.1488.23 2.39 0.30 T711; D2261-2 pH5; S5204; 0.41 5.14 2.23 88.44 2.39 0.45T711; D2261-24

TABLE 113 Fatty acid profile in some representative complemented (D2267)and parent S5204 lines transformed with pSZ3517 DNA containing PmAHI1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.34 4.87 2.11 90.00 1.20 0.39 T720; D2267-3pH5; S5204; 0.37 5.00 2.14 89.50 1.46 0.49 T720; D2267-20 pH5; S5204;0.34 4.90 2.08 89.75 1.67 0.36 T720; D2267-36 pH5; S5204; 0.37 4.95 2.1489.77 1.69 0.00 T720; D2267-15 pH5; S5204; 0.35 4.85 2.12 89.71 1.720.32 T720; D2267-2

TABLE 114 Fatty acid profile in some representative complemented (D2262)and parent S5204 lines transformed with pSZ3512 DNA containing PmCEP1pdriving PmFAD2-1. C18:3 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2 α pH7;S3150 1.71 29.58 3.13 56.53 6.43 0.68 pH5; S3150 1.56 27.70 2.98 59.495.95 0.53 pH7; S5204 0.30 5.59 1.63 90.88 0.1 0 pH5; S5204 0.39 5.671.36 91.13 0 0 pH5; S5204; 0.48 5.50 2.08 90.58 0.35 0.00 T711; D2262-3pH5; S5204; 0.39 5.20 2.17 89.90 1.08 0.37 T711; D2262-33 pH5; S5204;0.34 5.08 1.93 89.69 1.34 0.37 T711; D2262-24 pH5; S5204; 0.40 4.89 2.1989.88 1.45 0.27 T711; D2262-32 pH5; S5204; 0.39 4.95 2.75 89.30 1.470.27 T711; D2262-34

Combined baseline expression of endogenous PmFAD2-1 and PmFAD2-2 in wildtype Prototheca strains (like S3150, S1920 or S1331) manifests as 5-7%C18:2. S5204 overexpresses PmKASII which results in the elongation ofC16:0 to C18:0. This increased pool of C18:0 is eventually desaturatedby PmSAD2 resulting in elevated C18:1 levels. Additionally disruption ofthe both copies of PmFAD2 (viz. PmFAD2-1 and PmFAD2-2) in S5204 preventsfurther desaturation of C18:1 into C18:2 and results in a unique higholeic oil (C18:1) with 0% linoleic acid (C18:2). However as mentionedabove any strain with 0% C18:2 grows very poorly and requires exogenousaddition of linoleic acid to sustain growth/productivity.Complementation of a strain like S5204 with inducible PmAMT03p drivenPmFAD2-1 can rescue the growth phenotype while preserving the terminalhigh C18:1 with 0% C18:2 levels. However data suggests that PmAMT03shuts off in the early stages of fermentation thus severely compromisingthe ability of any complemented strain to achieve its full growth andproductivity potential. The goal of this work was to identify promoterelements that would allow the complemented strains to grow efficientlyin early stages of fermentation (TO-T30 hrs; irrespective of excessbatched N in the fermenters) and then effectively shut off once thecells enter active lipid production (when N in the media gets depleted)so that the complemented strains would still finish with very high C18:1and 0% C18:2 levels. As a comparator we also complemented S5204 withPmFAD2-1 being driven by either PmFAd2-1p or PmFAD2-2p promoterelements.

Complementation of S5204 with PmFAD2-1 driven by either PmFAD2-1p orPmFAD2-2p promoter elements results in complete restoration of the C18:2levels using vectors either designed to amplify PmFAD2-1 copy number(e.g. pSZ3375 or pSZ3376) or the ones where PmFAD2-1 copy number isrestricted to one (pSZ3382 or pSZ3383). Copy number of the PmFAD2-1 inthese strains seems to have very marginal effect on the terminal C18:2levels.

On the other hand expression of PmFAD2-1 driven by any of new promoterelements results in marked decrease in terminal C18:2 levels. Therepresentative profiles from various strains expressing new promotersdriving FAD2-1 are shown in Tables 84-114. This reduction in C18:2levels is even more pronounced in strains where the copy number ofPmFAD2-1 is limited to one. Promoter elements like PmDPS1 (D2091 &D2098), PmDPS2 (D2092 & D2099), PmPPI 1 (D2263 & D2440), PmPPI2 (D2264 &D2268), PmGMPS1 (D2265 & D2269), PmGMPS2 (D2270) resulted in strainswith 0% or less than 0.5% terminal C18:2 levels in both single ormultiple copy PmFAD2-1 versions. The rest of the promoters resulted interminal C18:2 levels that ranged between 1-5%. One unexpected resultwas the data from PmAHC1p and PmAHC2p driving PmFAD2-1 in D2434 andD2435. Both these promoters resulted in very high levels of C18:2(9-20%) in multiple copy FAD2-1 versions. The levels of terminal C18:2in single copy version in D2266 was more in line with the transcriptomicdata suggesting that PmAHC promoter activity and the corresponding PmAHCtranscription is severely downregulated when cells are activelyproducing lipid in depleted nitrogen environment. A quick look at thetranscriptome revealed that the initial transcription of PmAHC is veryhigh (4000-5500 TPM) which then suddenly drops down to 250 TPM. Thus itis conceivable that in strains with multiple copies on PmFAD2-1 (D2434and D2435), the massive amount of PmFAD2-1 protein produced earlier inthe fermentation lingers and results in high C18:2 levels. In singlecopy PmFAD2-1 strains this is not the case and thus we do not seeelevated C18:2 levels in D2266.

In complemented strains with 0% terminal C18:2 levels, the key questionwas whether they were complemented in the first place. In order toascertain that, representative strains along with parent S5204 andpreviously AMT03p driven PmFAD2-1 complemented S2532 (viz S4695) strainswere grown in seed medium in 96 well blocks. The cultures were seeded at0.1 OD units per ml and the OD750 was checked at different time points.Compared to S5204, which grew very poorly, only S4695 and newlycomplemented strains grew to any meaningful OD's at 20 and 44 hrs (Table115) demonstrating that the promoters identified above are active earlyon and switch off once cells enter the active lipid production phase.

TABLE 115 Growth characteristics of Δfad2 Δfata1 strain S5204, S4695 andrepresentative complemented S5204 lines in seed medium sorted by OD750at 44 hrs. Note that in 1 ml 96 well blocks after initial rapid divisionand growth, cells stop growing efficiently because of lack of nutrients,aeration etc. OD750 OD750 OD750 Sample ID C14:0 C16:0 C18:0 C18:1 C18:2C18:3α @20 hrs @44 hrs @68 hrs S5204 0.162 7.914 10.93 S5204 0.224 6.8549.256 S4695 1.456 29.032 32.766 pH7; S5204; T672; D2091-46 0.31 5.362.24 90.67 0.00 0.00 1.38 33.644 33.226 pH5; S5204; T720; D2268-1 0.396.43 1.78 90.49 0.00 0.00 0.75 32.782 31.624 S5204; 1720; D2270-47 0.396.69 1.81 90.05 0.00 0.00 1.204 32.752 31.602 pH5; S5204; T720; D2270-390.39 6.87 1.81 89.94 0.00 0.00 1.012 32.552 33.138 pH7; S5204; T680;D2099-35 0.30 4.56 1.54 92.49 0.00 0.00 0.48 32.088 31.92 pH5; S5204;T720; D2270-44 0.51 6.85 1.74 90.06 0.00 0.00 1.468 31.802 30.61 pH5;S5204; T720; D2270-41 0.00 7.85 1.65 89.18 0.00 0.00 1.576 31.35 30.69pH5; S5204; T720; D2270-17 0.46 6.78 1.71 90.24 0.00 0.00 1.79 30.73224.768 pH7; S5204; T680; D2099-30 0.32 4.59 1.57 92.40 0.00 0.00 0.5930.166 34.64 pH5; S5204; T720; D2268-40 0.42 6.66 1.86 90.02 0.00 0.000.764 29.62 29 pH5; S5204; T720; D2270-23 0.39 6.52 1.72 90.35 0.00 0.001.334 29.604 27.518 pH5; S5204; T720; D2270-42 0.61 6.59 1.53 90.28 0.000.00 2.042 28.986 32.184 pH7; S5204; T672; D2090-5 0.33 4.73 1.84 91.240.00 0.00 1.326 28.976 35.508 pH7; S5204; T672; D2091-15 0.30 5.26 2.2090.73 0.00 0.00 0.826 28.824 32.848 pH7; S5204; T680; D2099-20 0.31 4.021.46 93.07 0.00 0.00 1.31 28.732 26.61 pH5; S5204; T720; D2269-19 0.426.51 1.61 90.43 0.00 0.00 1.278 28.65 31.362 pH5; S5204; T720; D2269-290.43 7.36 1.72 89.35 0.00 0.00 1.342 28.376 28.66 pH5; S5204; T720;D2270-19 0.39 6.81 1.75 90.05 0.00 0.00 2.142 28.376 25.934 pH5; S5204;T720; D2270-43 0.80 7.64 1.66 88.93 0.00 0.00 1.896 28.174 32.376 pH5;S5204; T720; D2270-46 0.45 6.75 1.72 90.02 0.00 0.00 1.644 28.122 30.464pH5; S5204; T720; D2268-3 0.38 6.56 1.74 90.27 0.00 0.00 0.926 28.11431.552 pH5; S5204; T720; D2268-12 0.00 5.68 1.84 91.53 0.00 0.00 1.41428.106 30.644 pH5; S5204; T720; D2269-37 0.54 7.12 1.75 89.80 0.00 0.001.268 28.078 30.014 pH5; S5204; T720; D2270-31 0.46 6.94 1.74 89.71 0.000.00 1.224 28.064 29.344 pH5; S5204; T720; D2270-48 0.00 7.21 1.87 90.160.00 0.00 1.352 28 28.21 pH5; S5204; T720; D2269-8 0.33 6.67 1.64 90.340.00 0.00 0.96 27.912 27.564 pH5; S5204; T720; D2268-32 0.44 6.59 1.8590.11 0.00 0.00 0.78 27.834 31.952 pH5; S5204; T720; D2269-47 0.42 6.831.82 89.85 0.00 0.00 1.17 27.76 29.648 pH7; S5204; T672; D2091-19 0.314.51 1.77 91.65 0.00 0.00 1.568 27.682 25.828 pH5; S5204; T720; D2270-380.39 6.65 1.83 90.11 0.00 0.00 1.74 27.606 31.104 pH5; S5204; T720;D2268-2 0.38 6.49 1.74 90.38 0.00 0.00 0.95 27.564 32.254 pH5; S5204;T720; D2269-35 0.38 7.04 1.68 89.82 0.00 0.00 1.19 27.482 29.186 pH5;S5204; T720; D2269-20 0.36 7.01 1.73 89.86 0.00 0.00 0.966 27.47 28.284pH5; S5204; T720; D2269-13 0.39 6.76 1.89 89.98 0.00 0.00 0.936 27.3933.464 pH7; S5204; T680; D2099-24 0.28 4.67 1.50 92.38 0.00 0.00 0.827.28 27.35 pH5; S5204; T720; D2268-11 0.38 6.56 1.85 90.56 0.00 0.001.136 27.254 32.508 pH5; S5204; T720; D2270-3 0.41 6.69 1.70 90.22 0.000.00 0.872 27.214 30.23 pH5; S5204; T720; D2269-33 0.39 6.36 1.67 90.590.00 0.00 0.956 27.194 30.568 pH5; S5204; T720; D2268-10 0.45 6.93 1.7090.16 0.00 0.00 0.612 27.126 31.616 pH5; S5204; T720; D2269-43 0.36 6.551.84 90.25 0.00 0.00 0.998 27.086 29.618 pH5; S5204; T720; D2270-1 0.376.80 1.74 90.18 0.00 0.00 2.428 27.004 31.044 pH5; S5204; T720; D2268-40.45 5.73 1.52 91.75 0.00 0.00 0.736 26.948 28.796 pH5; S5204; T720;D2270-9 0.38 6.88 1.74 90.22 0.00 0.00 2.68 26.944 29.92 pH5; S5204;T720; D2269-26 0.41 6.85 1.68 90.03 0.00 0.00 0.896 26.794 31.31 pH5;S5204; T720; D2270-24 0.39 6.51 1.78 90.33 0.00 0.00 1.51 26.682 27.486pH5; S5204; T720; D2269-18 0.41 7.04 1.71 89.83 0.00 0.00 1.024 26.5829.794 pH5; S5204; T720; D2269-32 0.38 6.81 1.72 90.06 0.00 0.00 1.21426.48 29.478 pH5; S5204; T720; D2268-31 0.33 6.68 1.76 90.20 0.00 0.000.808 26.432 31.294 pH5; S5204; T720; D2269-7 0.29 5.33 1.69 91.59 0.000.00 1.1 26.41 28.754 pH5; S5204; T720; D2268-6 0.39 6.62 1.70 90.280.00 0.00 0.626 26.372 30.822 pH7; S5204; T680; D2099-27 0.40 4.07 1.2293.26 0.00 0.00 0.936 26.116 29.75 pH5; S5204; T720; D2269-39 0.48 6.881.82 89.67 0.00 0.00 2.218 26.106 30.8 pH5; S5204; T720; D2269-12 0.356.39 1.80 90.47 0.00 0.00 1.18 26.032 28.19 pH5; S5204; T720; D2269-420.39 6.99 1.67 89.91 0.00 0.00 2.132 25.924 27.854 pH5; S5204; T720;D2268-8 0.56 6.77 1.49 90.20 0.00 0.00 0.96 25.702 29.788 pH5; S5204;T720; D2270-37 0.44 7.33 1.71 89.69 0.00 0.00 0.916 25.612 34.034 pH5;S5204; T720; D2270-40 0.00 9.30 1.62 88.12 0.00 0.00 2.072 25.552 29.474pH5; S5204; T720; D2270-14 0.43 7.40 1.71 89.73 0.00 0.00 1.916 25.52627.908 pH5; S5204; T720; D2269-21 0.40 6.69 1.69 89.99 0.00 0.00 0.82625.396 29 pH5; S5204; T718; D2265-16 0.46 7.02 1.71 90.06 0.00 0.00 0.925.332 32.018 pH5; S5204; T720; D2270-15 0.40 6.90 1.68 90.32 0.00 0.001.594 25.32 26.794 pH5; S5204; T720; D2269-40 0.00 7.00 1.66 90.15 0.000.00 1.804 25.286 29.468 pH5; S5204; T720; D2268-5 0.38 6.58 1.81 90.790.00 0.00 0.678 25.156 33.066 pH5; S5204; T720; D2270-18 0.45 6.20 1.4591.09 0.00 0.00 2.646 25.126 27.536 pH5; S5204; T720; D2269-25 0.44 7.021.69 89.91 0.00 0.00 0.868 25.018 32.104 pH5; S5204; T720; D2269-30 0.456.77 1.78 90.00 0.00 0.00 0.718 24.978 29.868 pH5; S5204; T720; D2270-250.31 6.82 1.68 90.09 0.00 0.00 2.32 24.814 36.024 pH5; S5204; T720;D2270-21 0.52 7.23 1.70 89.99 0.00 0.00 1.92 24.58 25.398 pH5; S5204;T720; D2269-38 0.00 7.45 1.50 90.19 0.00 0.00 1.494 24.578 30.178 pH5;S5204; T720; D2268-9 0.48 5.94 1.51 90.83 0.00 0.00 0.73 24.344 30.83pH5; S5204; T720; D2268-37 0.44 6.35 1.84 90.31 0.00 0.00 0.548 24.30632.848 pH5; S5204; T720; D2269-28 0.41 7.12 1.66 89.73 0.00 0.00 0.80824.288 31.27 pH5; S5204; T720; D2270-5 0.44 6.98 1.78 89.79 0.00 0.002.328 24.14 30.186 pH5; S5204; T720; D2269-23 0.44 6.99 1.71 89.43 0.000.00 0.876 24.076 29.494 pH5; S5204; T720; D2269-9 0.38 6.84 1.71 90.320.00 0.00 0.806 24 26.844 pH5; S5204; T720; D2269-24 0.55 7.31 1.7189.68 0.00 0.00 1.09 23.97 29.642 pH5; S5204; T720; D2270-35 0.36 6.581.72 90.38 0.00 0.00 1.554 23.71 28.868 pH5; S5204; T720; D2269-15 0.005.69 1.36 91.86 0.00 0.00 1.246 23.584 28.196 pH5; S5204; T720; D2270-280.39 7.15 1.82 89.92 0.00 0.00 1.648 23.486 30.858 pH7; S5204; T680;D2098-39 0.34 4.89 1.56 92.08 0.00 0.00 1.08 23.46 31.888 pH5; S5204;T720; D2269-27 0.33 6.87 1.68 89.98 0.00 0.00 1.3 23.262 33.112 pH5;S5204; T718; D2265-43 0.00 7.90 1.90 89.27 0.00 0.00 0.832 23.23 30.052pH5; S5204; T720; D2270-30 0.41 pH5; S5204; T720; D2269-22 0.39 7.121.72 89.63 0.00 0.00 1.08 22.634 27.532 pH5; S5204; T718; D2263-30 0.547.58 1.57 89.47 0.00 0.00 0.71 22.564 29.996 pH7; S5204; T672; D2091-470.32 5.22 2.23 90.45 0.00 0.00 0.938 22.486 32.046 pH5; S5204; T720;D2269-1 0.38 6.73 1.68 90.24 0.00 0.00 1.154 22.48 29.994 pH7; S5204;T673; D2096-6 0.33 4.18 1.10 92.91 0.00 0.00 0.91 22.446 28.714 pH5;S5204; T720; D2270-33 0.40 6.95 1.76 89.89 0.00 0.00 2.28 22.408 29.656pH5; S5204; T718; D2263-14 0.58 7.72 1.64 89.26 0.00 0.00 0.306 22.3532.294 pH5; S5204; T720; D2270-34 0.36 6.75 1.77 90.10 0.00 0.00 2.39822.3 28.958 pH7; S5204; T672; D2090-29 0.42 4.99 2.01 91.06 0.00 0.001.16 22.112 30.376 pH5; S5204; T720; D2269-14 0.00 7.86 1.80 89.57 0.000.00 0.574 21.802 31.558 pH5; S5204; T718; D2263-29 0.58 7.32 1.30 90.070.00 0.00 0.418 21.746 30.426 pH5; S5204; T718; D2263-19 0.62 7.92 1.5689.25 0.00 0.00 0.574 21.692 29.514 pH5; S5204; T720; D2269-10 0.39 6.821.70 90.05 0.00 0.00 1.104 21.622 25.264 pH5; S5204; T720; D2269-4 0.426.57 1.71 90.32 0.00 0.00 1.082 21.466 29.698 pH5; S5204; T720; D2270-40.43 7.44 1.72 89.31 0.00 0.00 1.758 21.446 32.656 pH5; S5204; T720;D2269-34 0.00 6.69 1.78 90.64 0.00 0.00 0.946 21.438 28.538 pH5; S5204;T720; D2270-16 0.39 7.08 1.71 89.70 0.00 0.00 1.592 21.422 27.72 pH5;S5204; T718; D2263-26 0.42 7.39 1.70 89.28 0.00 0.00 0.514 21.328 29.746pH5; S5204; T720; D2269-3 0.36 6.76 1.71 90.17 0.00 0.00 0.668 21.24229.74 pH5; S5204; T720; D2270-22 0.35 6.77 1.67 90.15 0.00 0.00 1.19421.026 25.084 pH5; S5204; T720; D2270-26 0.41 6.81 1.82 89.66 0.00 0.001.606 20.948 32.142 pH5; S5204; T720; D2270-10 0.46 6.98 1.80 90.03 0.000.00 0.792 20.728 28.264 pH5; S5204; T720; D2269-16 0.51 6.17 1.50 90.640.00 0.00 0.922 20.502 30.132 pH5; S5204; T720; D2270-8 0.50 6.95 1.4290.34 0.00 0.00 2.252 20.486 28.34 pH5; S5204; T720; D2270-2 0.46 6.761.83 89.90 0.00 0.00 0.97 20.366 31.758 pH5; S5204; T720; D2269-36 0.007.43 1.66 89.88 0.00 0.00 0.754 20.006 29.648 pH5; S5204; T720; D2269-310.72 9.29 1.86 86.92 0.00 0.00 2.062 19.002 27.61 pH5; S5204; T720;D2269-44 0.00 9.45 1.58 88.16 0.00 0.00 1.378 18.576 22.52 pH7; S5204;T672; D2091-14 0.27 4.79 2.24 90.94 0.00 0.00 0.93 18.1 30.434 pH5;S5204; T720; D2270-32 0.40 7.14 1.74 89.63 0.00 0.00 1.668 17.966 27.06pH5; S5204; T720; D2270-11 0.82 9.24 1.93 87.35 0.00 0.00 1.178 15.99828.196 pH5; S5204; T720; D2269-48 0.72 9.05 2.14 88.08 0.00 0.00 1.17214.694 25.384 pH5; S5204; T720; D2269-17 0.66 9.08 2.12 87.12 0.00 0.000.84 14.488 25.886 pH5; S5204; T720; D2270-20 0.62 8.35 1.97 88.43 0.000.00 1.37 14.168 23.794 pH5; S5204; T718; D2263-13 0.75 9.44 1.98 87.090.00 0.00 0.64 13.854 29.466 pH5; S5204; T720; D2269-46 0.43 6.87 1.7189.81 0.00 0.00 0.646 10.452 31.464 pH5; S5204; T720; D2269-5 0.59 8.811.93 87.97 0.00 0.00 0.654 9.37 25.786 pH7; S5204; T672; D2091-4 1.424.39 2.32 89.87 0.00 0.00 0.686 8.182 16.454 pH5; S5204; T720; D2269-60.50 7.29 1.73 89.29 0.00 0.00 0.79 7.978 21.346 pH5; S5204; T720;D2270-45 0.00 9.16 1.65 88.19 0.00 0.00 0.464 3.448 16.796 Blank 0 0 0

It is contemplated that these promoters, or variants thereof, discoveredhere can be used to regulate a fatty acid synthesis gene (e.g., any ofthe FATA, FATB, SAD, FAD2, KASI/IV, KASII, LPAAT or KCS genes disclosedherein) or other gene or gene-suppression element expressed in a cellincluding a microalgal cell. Variants can have for example 60, 65, 70,75, 80, 85, 90, 95, 96, 97, 98, 99% or greater identity to the sequencesdisclosed here.

Example 64 Fractionation of a High SOS Oil to Increase SOS Concentrationand Reduce Trisaturates

Microalgal oil was fractionated using dry fractionation and solventfractionation techniques. The starting material was an oil that was highin SOS triglycerides. The oil was produced from Prototheca moriformisstrain S7566, in which a the endogenous KASII gene was inserted into(and thereby knocking out) a SADII locus; additionally, theC18-preferring FATA1 gene from Garcinia mangostana was inserted and aFADII hairpin RNA was produced; as described above. After cultivationand extracted, the oil was refined, bleached and deodorized. The fattyacid profile of the oil is given in Table 115. The SOS TAG area% wasabout 62%. During the RBD processing, the total trisaturates (i.e.triglycerides with three fully saturated acyl chains such as SSS, PSS,PPS, PPP, etc.) in the oil decreased from 5.1% to 1.2%.

TABLE 116 Fatty acid profile of clarified oil from strain 7566. StrainS7566 Fatty Acid Area % C14:0 0.49 C16:0 3.12 C18:0 54.77 C18:l 35.88C18:2 2.16 C18:3 α 0.23 C20:0 1.64 C22:0 0.19 C24:0 0.11 sum C18 93.05saturates 60.69 unsaturates 38.55

The oil was fractionated using solvent (acetone or hexane) and dryfractionation. Acetone fractionation (1:1 oil-solvent, w/w;crystallization at 5° C.) gave excellent recovery of an SOS-enrichedstearin fraction, with relatively little SOS in the olein fraction. SOSwas at 77%, with total trisaturates <1% for the stearin fraction.

Hexane fractionation(1:1 oil-solvent, w/w; crystallization at 5° C.)gave a higher level (85%) of SOS, but also gave higher trisaturates(1.6%). Thus, using a single-step solvent fractionation, oils with over75% SOS and less than 2% trisaturates were obtainable.

Dry fractionation was also successful in enriching SOS and decreasingtrisaturates. The general approach was to remove trisaturates bycrystallization at a higher temperature, then removing 00S at a lowertemperature. The reverse order was also tried and yielded a superiorresult. It was also found that rinsing the SOS-enriched (“stearin”)fraction with acetone helped in removing the olein fraction.

In one test, the oil was crystallized at 24° C. and the stearin fractionwas rinsed with acetone. Analysis showed that 00S levels decreased. Thestearin fraction was heated and allowed to cool and crystallizeovernight at 29° C. The resulting liquid oil was separated from thecrystallized trisaturates to afford a product with 84% SOS and <0.5%total trisaturates. Lipase-based sn-2 profile analysis of revealed thatover 96% of that position was occupied by unsaturated fatty acids (93.3%oleate, 3.2% linolate, and 0.2% linolenate), while only 2.2% stearatewas located there.

The DSC heating curve thermogram and DSC-derived solid fat content curveof the two step dry fractionated oil was compared to those of kokumbutter. The two oils have essentially identical maximum heat-flowtemperatures and the DSC-derived SFC curves are super-imposable. The oilcould be expected to behave functionally similarly to kokum butter.

Example 65 Production of Microbial Oil with Over 60% SOS Content

Here, we demonstrate in the microalga Prototheca moriformis, that bydisrupting an allele of the SAD2 gene, overexpressing KASII, knockingout endogenous FATA-1, overexpressing a more stearate-specific FATA(GarmFATA1 from Garcinia mangostana) relative to the endogenous FATA andactivating FAD2 RNAi, we generate strains capable of accumulating over60% SOS, useful as a structuring fat.

To reduce SAD activity, Strain S3150 was transformed with DNA constructsdesigned to recombine in the SAD2-1 and SAD2-2 alleles and express theselectable marker, Arabidopsis thialiana THIC (AtTHIC, codon-optimizedfor expression in P. moriformis). THIC encodes4-amino-5-hydroxymethyl-2-methylpyrimidine synthase, thereby allowinggrowth in the absence of added thiamine. Transformants were selected inthe absence of exogenous thiamine.

To make the SAD2-1 ablation construct pSZ2601, the Arabidopsis thalianaTHIC gene (AtTHIC, codon-optimized for expression in P. moriformis), wasutilized as a selectable marker for transformation. The sequence of thetransforming DNA is shown in SEQ ID NO:148. Relevant restriction sitesare indicated in lowercase, bold, and are from 5′-3′ BspQI, PmeI, KpnI,XbaI, MfeI, SacI, BspQI and PmeI. Underlined sequences at the 5′ and 3′flanks of the construct represent genomic DNA from P. moriformis thatenable targeted integration of the transforming DNA via homologousrecombination at the SAD2-1 locus. Proceeding in the 5′ to 3′ direction,the Chlorella protothecoides ACT promoter (CpACT) driving the expressionof the AtTHIC gene (encoding 4-amino-5-hydroxymethyl-2-methylpyrimidinesynthase activity, thereby permitting the strain to grow in the absenceof exogenous thiamine) is indicated by lowercase, boxed text. Theinitiator ATG and terminator TGA for AtTHIC are indicated by uppercaseitalics, while the coding region is indicated with lowercase italics.The 3′ UTR of the Chlorella vulgaris nitrate reductase (CvNR) gene isindicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2601:(SEQ ID NO: 148) gaagagcgcccaatgtttaaacGCCGGTCACCACCCGCATGCTCGTACTACAGCGCACGCACCGCTTCGTGATCCACCGGGTGAACGTAGTCCTCGACGGAAACATCTGGTTCGGGCCTCCTGCTTGCACTCCCGCCCATGCCGACAACCTTTCTGCTGTTACCACGACCCACAATGCAACGCGACACGACCGTGTGGGACTGATCGGTTCACTGCACCTGCATGCAATTGTCACAAGCGCTTACTCCAATTGTATTCGTTTGTTTTCTGGGAGCAGTTGCTCGACCGCCCGCGTCCCGCAGGCAGCGATGACGTGTGCGTGGCCTGGGTGTTTCGTCGAAAGGCCAGCAACCCTAAATCGCAGGCGATCCGGAGATTGGGATCTGATCCGAGTTTGGACCAGATCCGCCCCGATGCGGCACGGGAACTGCATCGACTCGGCGCGGAACCCAGCTTTCGTAAATGCCAGATTGGTGTCCGATACCTGGATTTGCCATCAGCGAAACAAGACTTCAGCAGCGAGCGTATTTGGCGGGCGTGCTACCAGGGTTGCATACATTGCCCATTTCTGTCTGGACCGCTTTACTGGCGCAGAGGGTGAGTTGATGGGGTTGGCAGGCATCGAAACGCGCGTGCATGGTGTGCGTGTCTGTTTTCGGCTGCACGAATTCAATAGTCGGATGGGCGACGGTAGAATTGGGTGTGGCGCTCGCGTGCATGCCTCGCCCCGTCGGGTGTCATGACCGGGACTGGAATCCCCCCTCGCGACCATCTTGCTAACGCTCCCGACTCTCCCGACCGCG

gcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTG CTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAGGATCGTAgagctcTAGGGAGCGACGAGTGTGCGTGCGGGGCTGGCGGGAGTGGGACGCCCTCCTCGCTCCTCTCTGTTCTGAACGGAACAATCGGCCACCCCGCGCTACGCGCCACGCATCGAGCAACGAAGAAAACCCCCCGATGATAGGTTGCGGTGGCTGCCGGGATATAGATCCGGCCGCACATCAAAGGGCCCCTCCGCCAGAGAAGAAGCTCCTTTCCCAGCAGACTCCTTCTGCTGCCAAAACACTTCTCTGTCCACAGCAACACCAAAGGATGAACAGATCAACTTGCGTCTCCGCGTAGCTTCCTCGGCTAGCGTGCTTGCAACAGGTCCCTGCACTATTATCTTCCTGCTTTCCTCTGAATTATGCGGCAGGCGAGCGCTCGCTCTGGCGAGCGCTCCTTCGCGCCGCCCTCGCTGATCGAGTGTACAGTCAATGAATGGTCCTGGGCGAAGAACGAGGGAATTTGTGGGTAAAACAAGCATCGTCTCTCAGGCCCCGGCGCAGTGGCCGTTAAAGTCCAAGACCGTGACCAGGCAGCGCAGCGCGTCCGTGTGCGGGCCCTGCCTGGCGGCTCGGCGTGCCAGGCTCGAGAGCAGCTCCCTCAGGTCGCCTTGGACGGCCTCTGCGAGGCCGGTGAGGGCCTGCAGGAGCGCCTCGAGCGTGGCAGTGGCGGTCGTATCCGGGTCGCCGGTCACCGCCTGCGACTCGCCATCC gaagagcgtttaaac

The sequence of the transforming DNA from the SAD2-1 disruptionconstruct, pSZ2607, is shown below in SEQ ID NO:149. Relevantrestriction sites are indicated in lowercase, bold, and are from 5′-3′PmeI, KpnI, XbaI, MfeI, SacI, BspQI and PmeI. Underlined sequences atthe 5′ and 3′ flanks of the construct represent genomic DNA from P.moriformis that enable targeted integration of the transforming DNA viahomologous recombination at the SAD2-1 locus. Proceeding in the 5′ to 3′direction, the Chlorella protothecoides ACT promoter (CpACT) driving theexpression of the AtTHIC gene (encoding4-amino-5-hydroxymethyl-2-methylpyrimidine synthase activity, therebypermitting the strain to grow in the absence of exogenous thiamine) isindicated by lowercase, boxed text. The initiator ATG and terminator TGAfor AtTHIC are indicated by uppercase italics, while the coding regionis indicated with lowercase italics. The 3′ UTR of the Chlorellavulgaris nitrate reductase (CvNR) gene is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2607:(SEQ ID NO: 149) gtttaaacGCCGGTCACCACCCGCATGCTCGTACTACAGCGCACGCACCGCTTCGTGATCCACCGGGTGAACGTAGTCCTCGACGGAAACATCTGGTTCGGGCCTCCTGCTTGCACTCCCGCCCATGCCGACAACCTTTCTGCTGTTACCACGACCCACAATGCAACGCGACACGACCGTGTGGGACTGATCGGTTCACTGCACCTGCATGCAATTGTCACAAGCGCTTACTCCAATTGTATTCGTTTGTTTTCTGGGAGCAGTTGCTCGACCGCCCGCGTCCCGCAGGCAGCGATGACGTGTGCGTGGCCTGGGTGTTTCGTCGAAAGGCCAGCAACCCTAAATCGCAGGCGATCCGGAGATTGGGATCTGATCCGAGTTTGGACCAGATCCGCCCCGATGCGGCACGGGAACTGCATCGACTCGGCGCGGAACCCAGCTTTCGTAAATGCCAGATTGGTGTCCGATACCTGGATTTGCCATCAGCGAAACAAGACTTCAGCAGCGAGCGTATTTGGCGGGCGTGCTACCAGGGTTGCATACATTGCCCATTTCTGTCTGGACCGCTTTACTGGCGCAGAGGGTGAGTTGATGGGGTTGGCAGGCATCGAAACGCGCGTGCATGGTGTGCGTGTCTGTTTTCGGCTGCACGAATTCAATAGTCGGATGGGCGACGGTAGAATTGGGTGTGGCGCTCGCGTGCATGCCTCGCCCCGTCGGGTGTCATGACCGGGACTGGAATCCCCCCTCGCGACCATCTTGCTAACGCTCCCGACTCTCCCGACCGCGCGCAGGATAGA

gccgcgtccgtccactgcaccctgatgtccgtggtctgcaacaacaagaaccactccgcccgccccaagctgcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAAcAcAAATGGAGGATCGTAgagctcCAGCCACGGCAACACCGCGCGCCTTGCGGCCGAGCACGGCGACAAGAACCTGAGCAAGATCTGCGGGCTGATCGCCAGCGACGAGGGCCGGCACGAGATCGCCTACACGCGCATCGTGGACGAGTTCTTCCGCCTCGACCCCGAGGGCGCCGTCGCCGCCTACGCCAACATGATGCGCAAGCAGATCACCATGCCCGCGCACCTCATGGACGACATGGGCCACGGCGAGGCCAACCCGGGCCGCAACCTCTTCGCCGACTTCTCCGCGGTCGCCGAGAAGATCGACGTCTACGACGCCGAGGACTACTGCCGCATCCTGGAGCACCTCAACGCGCGCTGGAAGGTGGACGAGCGCCAGGTCAGCGGCCAGGCCGCCGCGGACCAGGAGTACGTCCTGGGCCTGCCCCAGCGCTTCCGGAAACTCGCCGAGAAGACCGCCGCCAAGCGCAAGCGCGTCGCGCGCAGGCCCGTCGCCTTCTCCTGGATCTCCGGGCGCGAGATCATGGTCTAGGGAGCGACGAGTGTGCGTGCGGGGCTGGCGGGAGTGGGACGCCCTCCTCGCTCCTCTCTGTTCTGAACGGAACAATCGGCCACCCCGCGCTACGCGCCACGCATCGAGCAACGAAGAAAACCCCCCGATGATAGGTTGCGGTGGCTGCCGGGATATAGATCCGGCCGCACATCAAAGGGCCCCTCCGCCAGAGAAGAAGCTCCTTTCCCAGCAGACTCCT gaagagcgtttaaac

The sequence of the transforming DNA from the SAD2-2 disruptionconstruct,pSZ2622, is shown below in SEQ ID NO:150. Relevant restrictionsites are indicated in lowercase, bold, and are from 5′-3′ BspQI, PmeI,KpnI, XbaI, MfeI, SacI, BspQI and PmeI. Underlined sequences at the 5′and 3′ flanks of the construct represent genomic DNA from P. moriformisthat enable targeted integration of the transforming DNA via homologousrecombination at the SAD2-1 locus. Proceeding in the 5′ to 3′ direction,the Chlorella protothecoides ACT promoter (CpACT) driving the expressionof the AtTHIC gene (encoding 4-amino-5-hydroxymethyl-2-methylpyrimidinesynthase activity, thereby permitting the strain to grow in the absenceof exogenous thiamine) is indicated by lowercase, boxed text. Theinitiator ATG and terminator TGA for AtTHIC are indicated by uppercaseitalics, while the coding region is indicated with lowercase italics.The 3′ UTR of the Chlorella vulgaris nitrate reductase (CvNR) gene isindicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2622:(SEQ ID NO: 150) gaagagcgcccaatgtttaaacGCCGGTCACCATCCGCATGCTCATATTACAGCGCACGCACCGCTTCGTGATCCACCGGGTGAACGTAGTCCTCGACGGAAACATCTGGCTCGGGCCTCGTGCTGGCACTCCCTCCCATGCCGACAACCTTTCTGCTGTCACCACGACCCACGATGCAACGCGACACGACCCGGTGGGACTGATCGGTTCACTGCACCTGCATGCAATTGTCACAAGCGCATACTCCAATCGTATCCGTTTGATTTCTGTGAAAACTCGCTCGACCGCCCGCGTCCCGCAGGCAGCGATGACGTGTGCGTGACCTGGGTGTTTCGTCGAAAGGCCAGCAACCCCAAATCGCAGGCGATCCGGAGATTGGGATCTGATCCGAGCTTGGACCAGATCCCCCACGATGCGGCACGGGAACTGCATCGACTCGGCGCGGAACCCAGCTTTCGTAAATGCCAGATTGGTGTCCGATACCTTGATTTGCCATCAGCGAAACAAGACTTCAGCAGCGAGCGTATTTGGCGGGCGTGCTACCAGGGTTGCATACATTGCCCATTTCTGTCTGGACCGCTTTACCGGCGCAGAGGGTGAGTTGATGGGGTTGGCAGGCATCGAAACGCGCGTGCATGGTGTGTGTGTCTGTTTTCGGCTGCACAATTTCAATAGTCGGATGGGCGACGGTAGAATTGGGTGTTGCGCTCGCGTGCATGCCTCGCCCCGTCGGGTGTCATGACCGGGACTGGAATCCCCCCTCGCGACCCTCCTGCTAACGCTCCCGACTCTCCCGCCCGCGCG

cccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGAcaattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAGGATCGTAgagctcCAGCCACGGCAACACCGCGCGCCTGGCGGCCGAGCACGGCGACAAGGGCCTGAGCAAGATCTGCGGGCTGATCGCCAGCGACGAGGGCCGGCACGAGATCGCCTACACGCGCATCGTGGACGAGTTCTTCCGCCTCGACCCCGAGGGCGCCGTCGCCGCCTACGCCAACATGATGCGCAAGCAGATCACCATGCCCGCGCACCTCATGGACGACATGGGCCACGGCGAGGCCAACCCGGGCCGCAACCTCTTCGCCGACTTCTCCGCCGTCGCCGAGAAGATCGACGTCTACGACGCCGAGGACTACTGCCGCATCCTGGAGCACCTCAACGCGCGCTGGAAGGTGGACGAGCGCCAGGTCAGCGGCCAGGCCGCCGCGGACCAGGAGTACGTTCTGGGCCTGCCCCAGCGCTTCCGGAAACTCGCCGAGAAGACCGCCGCCAAGCGCAAGCGCGTCGCGCGCAGGCCCGTCGCCTTCTCCTGGATCTCCGGACGCGAGATTATGGTCTAGGGAGGTACGAGCGCGCGCGAGGGATTGGTGGGAGTGGGACGCGCTCGTCGCTCCTTTCTATTCTGAAGGGAAGATTGGCCACCCCGCTCCACGCGCCACGCATCGAGCAACGAAGAAAACCCCCCGATGATAGGTTGCAGTGGCTGCCGAGATATAGATCCGGCTGCACGTCAAAGGGCCCCTCGGCCAGAGAAGAAGCTCTTTTCCCAGCGACCGCAGACTCC Tgaagagcgtttaaac

Constructs D1557, D1565 and D1566, derived from pSZ2601, pSZ2607 andpSZ2622, respectively, were transformed into S3150 as describedpreviously. Primary transformants were clonally purified and grown underlow-nitrogen lipid production conditions at pH 5. The resulting fattyacid profiles from representative clones are summarized in Table 117.SAD2-1 disruption strains derived from D1557 and D1565 transformantsaccumulated up to 13.4% C18:0 at the expense of C18:1, indicating thatSAD activity was significantly reduced in these strains. C18:0 levelsonly increased to 8.5% in SAD2-2 disruption strains, suggesting that theexpression or activity of SAD2-2 was lower than that of SAD2-1. We alsoobserved that C20:0 levels increased up to 1.1% in strains with elevatedC18:0, demonstrating that C18:0 was an effective primer for fatty acidelongation reactions in the endoplasmic reticulum (ER).

TABLE 117 Fatty acid profiles from representative clones. Strain S3150D1557-2 D1557-3 D1565-10 D1565-3 D1565-8 D1566-5 D1566-6 D1566-1 FattyC14:0 1.30 1.14 1.20 1.08 1.12 1.11 1.18 1.12 1.21 Acid C16:0 28.7129.32 29.74 28.84 29.34 29.11 29.21 29.13 28.46 Area C16:1 0.76 0.210.23 0.21 0.21 0.21 0.32 0.31 0.31 % C17:0 0.12 0.14 0.15 0.15 0.14 0.140.14 0.16 0.14 C18:0 2.93 13.42 11.92 14.29 14.14 14.04 8.47 8.47 7.68C18:1 58.08 46.29 47.65 45.75 45.31 45.69 51.29 51.33 53.38 C18:2 6.817.15 6.96 7.09 7.18 7.19 7.25 7.34 6.92 C18:3 α 0.59 0.69 0.63 0.72 0.720.73 0.71 0.73 0.62 C20:0 0.24 0.93 0.84 1.10 1.09 1.04 0.75 0.77 0.63C22:0 0.05 0.16 0.15 0.19 0.19 0.18 0.14 0.14 0.11 C24:0 0.06 0.16 0.160.20 0.20 0.20 0.17 0.17 0.14 sum C18 68.40 67.55 67.16 67.85 67.3567.65 67.72 67.87 68.60 saturates 33.49 45.35 44.24 45.94 46.32 45.9340.18 40.04 38.48 unsaturates 66.52 54.62 55.76 54.04 53.68 54.07 59.8359.97 61.50

In order to increase C18:0 accumulation at the expense of C16:0 wegenerated DNA constructs which simultaneously ablated SAD2-1 andover-expressed a codon-optimized version of the endogenousβ-ketoacyl-ACP synthase II (PmKASII) gene. The sequence of thetransforming DNA from the SAD2-1 ablation, PmKASII over-expressionconstruct, pSZ2624, is shown below in SEQ ID NO:151. Relevantrestriction sites are indicated in lowercase, bold, and are from 5′-3′PmeI, SpeI, AscI, ClaI, SacI, AvrII, EcoRV, AflII, KpnI, XbaI, MfeI,BamHI, BspQI and PmeI. Underlined sequences at the 5′ and 3′ flanks ofthe construct represent genomic DNA from P. moriformis that enabletargeted integration of the transforming DNA via homologousrecombination at the SAD2-1 locus. The SAD2-1 5′ integration flankcontained the endogeneous SAD2-1 promoter, enabling the in situactivation of the PmKASII gene. Proceeding in the 5′ to 3′ direction,the region encoding the PmKASII plastid targeting sequence is indicatedby lowercase, underlined italics. The sequence that encodes the maturePmKASII polypeptide is indicated with lowercase italics, while a 3× FLAGepitope encoding sequence is in bold italics. The initiator ATG andterminator TGA for PmKASII-FLAG are indicated by uppercase italics. Twospacer regions are represented by lowercase text. The CpACT promoterdriving the expression of the AtTHIC gene is indicated by lowercase,boxed text. The initiator ATG and terminator TGA for AtTHIC areindicated by uppercase italics, while the coding region is indicatedwith lowercase italics. The 3′ UTR of the Chlorella vulgaris nitratereductase (CvNR) gene is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ2624:(SEQ ID NO: 151) gtttaaacGCCGGTCACCACCCGCATGCTCGTACTACAGCGCACGCACCGCTTCGTGATCCACCGGGTGAACGTAGTCCTCGACGGAAACATCTGGTTCGGGCCTCCTGCTTGCACTCCCGCCCATGCCGACAACCTTTCTGCTGTTACCACGACCCACAATGCAACGCGACACGACCGTGTGGGACTGATCGGTTCACTGCACCTGCATGCAATTGTCACAAGCGCTTACTCCAATTGTATTCGTTTGTTTTCTGGGAGCAGTTGCTCGACCGCCCGCGTCCCGCAGGCAGCGATGACGTGTGCGTGGCCTGGGTGTTTCGTCGAAAGGCCAGCAACCCTAAATCGCAGGCGATCCGGAGATTGGGATCTGATCCGAGTTTGGACCAGATCCGCCCCGATGCGGCACGGGAACTGCATCGACTCGGCGCGGAACCCAGCTTTCGTAAATGCCAGATTGGTGTCCGATACCTGGATTTGCCATCAGCGAAACAAGACTTCAGCAGCGAGCGTATTTGGCGGGCGTGCTACCAGGGTTGCATACATTGCCCATTTCTGTCTGGACCGCTTTACTGGCGCAGAGGGTGAGTTGATGGGGTTGGCAGGCATCGAAACGCGCGTGCATGGTGTGCGTGTCTGTTTTCGGCTGCACGAATTCAATAGTCGGATGGGCGACGGTAGAATTGGGTGTGGCGCTCGCGTGCATGCCTCGCCCCGTCGGGTGTCATGACCGGGACTGGAATCCCCCCTCGCGACCATCTTGCTAACGCTCCCGACTCTCCCGACCGCGCGCAGGATAGACTCTTGTTCAACCAATCGACA actagtATGcagaccgcccaccagcgcccccccaccgagggccactgcttcggcgcccgcctgcccaccgcctcccgccgcgccgtgcgccgcgcctggtcccgcatcgcccgcgggcgcgccgccgccgccgccgacgccaaccccgcccgccccgagcgccgcgtggtgatcaccggccagggcgtggtgacctccctgggccagaccatcgagcagttctactcctccctgctggagggcgtgtccggcatctcccagatccagaagttcgacaccaccggctacaccaccaccatcgccggcgagatcaagtccctgcagctggacccctacgtgcccaagcgctgggccaagcgcgtggacgacgtgatcaagtacgtgtacatcgccggcaagcaggccctggagtccgccggcctgcccatcgaggccgccggcctggccggcgccggcctggaccccgccctgtgcggcgtgctgatcggcaccgccatggccggcatgacctccttcgccgccggcgtggaggccctgacccgcggcggcgtgcgcaagatgaaccccttctgcatccccttctccatctccaacatgggcggcgccatgctggccatggacatcggcttcatgggccccaactactccatctccaccgcctgcgccaccggcaactactgcatcctgggcgccgccgaccacatccgccgcggcgacgccaacgtgatgctggccggcggcgccgacgccgccatcatcccctccggcatcggcggcttcatcgcctgcaaggccctgtccaagcgcaacgacgagcccgagcgcgcctcccgcccctgggacgccgaccgcgacggcttcgtgatgggcgagggcgccggcgtgctggtgctggaggagctggagcacgccaagcgccgcggcgccaccatcctggccgagctggtgggcggcgccgccacctccgacgcccaccacatgaccgagcccgacccccagggccgcggcgtgcgcctgtgcctggagcgcgccctggagcgcgcccgcctggcccccgagcgcgtgggctacgtgaacgcccacggcacctccacccccgccggcgacgtggccgagtaccgcgccatccgcgccgtgatcccccaggactccctgcgcatcaactccaccaagtccatgatcggccacctgctgggcggcgccggcgccgtggaggccgtggccgccatccaggccctgcgcaccggctggctgcaccccaacctgaacctggagaaccccgcccccggcgtggaccccgtggtgctggtgggcccccgcaaggagcgcgccgaggacctggacgtggtgctgtccaactccttcggcttcggcggccacaactcctgcgtgatcttccgcaagtacgacgagatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag TGAatcgatAGATCTCTTAAGGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAAAGCTTAATTAAgagctccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgatggtcgaacgttcacagcctaggtgatatccatcttaaggatctaagtaagattcgaagcgctcgaccgtgccggacggactgcagccccatgtcgtagtgaccgccaatgtaagtgggctggcgtttccctgtacgtgagtcaacgtcactgcacgcgcaccaccctctcgaccggcaggaccaggcatcgcgag

ccaagctgcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGAcaattgACGGAGCGTCGTGCGGGAGGGAGTGTGCCGAGCGGGGAGTCCCGGTCTGTGCGAGGCCCGGCAGCTGACGCTGGCGAGCCGTACGCCCCGAGGGICCCCCTCCCCTGCACCCICTICCCCTICCCTCTGACGGCCGCGCCTGITCTTGCATGITCAGCGACggatccTAGGGAGCGACGAGTGTGCGTGCGGGGCTGGCGGGAGTGGGACGCCCTCCTCGCTCCTCTCTGTTCTGAACGGAACAATCGGCCACCCCGCGCTACGCGCCACGCATCGAGCAACGAAGAAAACCCCCCGATGATAGGTTGCGGTGGCTGCCGGGATATAGATCCGGCCGCACATCAAAGGGCCCCTCCGCCAGAGAAGAAGCTCCTTTCCCAGCAGACTCCTTCTGCTGCCAAAACACTTCTCTGTCCACAGCAACACCAAAGGATGAACAGATCAACTTGCGTCTCCGCGTAGCTTCCTCGGCTAGCGTGCTTGCAACAGGTCCCTGCACTATTATCTTCCTGCTTTCCTCTGAATTATGCGGCAGGCGAGCGCTCGCTCTGGCGAGCGCTCCTTCGCGCCGCCCTCGCTGATCGAGTGTACAGTCAATGAATGGTCCTGGGCGAAGAACGAGGGAATTTGTGGGTAAAACAAGCATCGTCTCTCAGGCCCCGGCGCAGTGGCCGTTAAAGTCCAAGACCGTGACCAGGCAGCGCAGCGCGTCCGTGTGCGGGCCCTGCCTGGCGGCTCGGCGTGCCAGGCTCGAGAGCAGCTCCCTCAGGTCGCCTTGGACGGCCTCTGCGAGGCCGGTGAGGGCCTGCAGGAGCGCCTCGAGCGTGGCAGTGGCGGTCGTATCCGGGTCGCCGGTCACCGCCTGCGACTCGCCATCCgaagagcgtttaaac

Using the methods of this example, by overexpressing KASII, and Garciniamangostana FATA, and by reducing expression of endogenous SAD, FAD2, andFATA, we produced a strain of P. moriformis that produced and oil withgreater than 55% SOS with Sat-O-Sat (where O is oleate and Sat is anysaturated fatty acid) of about 70-75% and trisaturatated TAGs of lessthan 6.5%.

Example 66 Combining KASII, FATA and LPAAT Transgenes to Produce an OilHigh in SOS

In Prototheca moriformis, we overexpressed the P. moriformis KASII,knocked out an endogenous SAD2 allele, knocked out the endogenous FATAallele, and overexpressed both a LPAAT from Brassica napus and a FATAgene from Garcinia mangostana (“GarmFAT1”). The resulting strainproduced an oil with over 55% SOS, over 70% Sat-O-Sat, and less than 8%trisaturated TAGs.

A base strain was transformed with a linearized plasmid with flankingregions designed for homologous recombination at the SAD2 site. As inexamples above, the construct ablated SAD2 and overexpressed P.moriformis KASII. A ThiC selection marker was used. This strain wasfurther transformed with a construct designed to overexpress GarmFATA1with a P. moriformis SASD1 plastid targeting peptide via homologousrecombination at the 6S chromosomal site using invertase as a selectionmarker. The resulting strain, produced oil with about 62% stearate, 6%palmitate, 5% linoleate, 45% SOS and 20% trisaturates.

The sequence of the transforming DNA from the GarmFATA1 expressionconstruct (pSZ3204) is shown below in SEQ ID NO:152. Relevantrestriction sites are indicated in lowercase, bold, and are from 5′-3′BspQI, KpnI, XbaI, MfeI, BamHI, AvrII, EcoRV, SpeI, AscI, ClaI, AflII,SacI and BspQI. Underlined sequences at the 5′ and 3′ flanks of theconstruct represent genomic DNA from P. moriformis that enable targetedintegration of the transforming DNA via homologous recombination at the6S locus. Proceeding in the 5′ to 3′ direction, the CrTUB2 promoterdriving the expression of Saccharomyces cerevisiae SUC2 (ScSUC2) gene,enabling strains to utilize exogenous sucrose, is indicated bylowercase, boxed text. The initiator ATG and terminator TGA of ScSUC2are indicated by uppercase italics, while the coding region isrepresented by lowercase italics. The 3′ UTR of the CvNR gene isindicated by small capitals. A spacer region is represented by lowercasetext. The P. moriformis SAD2-2 (PmSAD2-2) promoter driving theexpression of the chimeric CpSAD1tp_GarmFATA1 FLAG gene is indicated bylowercase, boxed text. The initiator ATG and terminator TGA areindicated by uppercase italics; the sequence encoding CpSAD1tp isrepresented by lowercase, underlined italics; the sequence encoding theGarmFATA1 mature polypeptide is indicated by lowercase italics; and the3× FLAG epitope tag is represented by uppercase, bold italics. A secondCvNR 3′ UTR is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ3204:(SEQ ID NO:  152) gctcttcGCCGCCGCCACTCCTGCTCGAGCGCGCCCGCGCGTGCGCCGCCAGCGCCTTGGCCTTTTCGCCGCGCTCGTGCGCGTCGCTGATGTCCATCACCAGGTCCATGAGGTCTGCCTTGCGCCGGCTGAGCCACTGCTTCGTCCGGGCGGCCAAGAGGAGCATGAGGGAGGACTCCTGGTCCAGGGTCCTGACGTGGTCGCGGCTCTGGGAGCGGGCCAGCATCATCTGGCTCTGCCGCACCGAGGCCGCCTCCAACTGGTCCTCCAGCAGCCGCAGTCGCCGCCGACCCTGGCAGAGGAAGACAGGTGAGGGGGGTATGAATTGTACAGAACAACCACGAGCCTTGTCTAGGCAGAATCCCTACCAGTCATGGCTTTACCTGGATGACGGCCTGCGAACAGCTGTCCAGCGACCCTCGCTGCCGCCGCTTCTCCCGCACGCTTCTTTCCAGCACCGTGATGGCGCGAGCCAGCGCCGCACGCTGGCGCTGCGCTTCGCCGATCTGAGGACAGTCGGGGAACTCTGATCAGTCTAAACCCCCTTGCGCGTTAGTGTTGCCATCCTTTGCAGACCGGTGAGAGCCGACTTGTTGTGCGCCACCCCCCACACCACCTCCTCCCAGACCAATTCTGTCACCTTTTTGGCGAAGGCATCGGCCTCGGCC

gcttcgccgccaagatcagcgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGA caattgGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttggcgaggtggcaggtgacaatgatcggtggagctgat

actagt ATGgccaccgcatccactttctcggcgttcaatgcccgctgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcg ggcgcgccatccccccccgcatcatcgtggtgtcctcctcctcctccaaggtgaaccccctgaagaccgaggccgtggtgtcctccggcctggccgaccgcctgcgcctgggctccctgaccgaggacggcctgtcctacaaggagaagttcatcgtgcgctgctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtgggctgcaaccacgcccagtccgtgggctactccaccggcggcttctccaccacccccaccatgcgcaagctgcgcctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtggtggagatcgagtcctggggccagggcgagggcaagatcggcacccgccgcgactggatcctgcgcgactacgccaccggccaggtgatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagaaggtggacgtggacgtgcgcgacgagtacctggtgcactgcccccgcgagctgcgcctggccttccccgaggagaacaactcctccctgaagaagatctccaagctggaggacccctcccagtactccaagctgggcctggtgccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatgccccaggagatcatcgacacccacgagctgcagaccatcaccctggactaccgccgcgagtgccagcacgacgacgtggtggactccctgacctcccccgagccctccgaggacgccgaggccgtgttcaaccacaacggcaccaacggctccgccaacgtgtccgccaacgaccacggctgccgcaacttcctgcacctgctgcgcctgtccggcaacggcctggagatcaaccgcg

CGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAAcAcAAATGGAaagcttaattaagagctcTTGTTTTCCAGAAGGAGTTGCTCCTTGAGCCTTTCATTCTCAGCCTCGATAACCTCCAAAGCCGCTCTAATTGTGGAGGGGGTTCGAATTTAAAAGCTTGGAATGTTGGTTCGTGCGTCTGGAACAAGCCCAGACTTGTTGCTCACTGGGAAAAGGACCATCAGCTCCAAAAAACTTGCCGCTCAAACCGCGTACCTCTGCTTTCGCGCAATCTGCCCTGTTGAAATCGCCACCACATTCATATTGTGACGCTTGAGCAGTCTGTAATTGCCTCAGAATGTGGAATCATCTGCCCCCTGTGCGAGCCCATGCCAGGCATGTCGCGGGCGAGGACACCCGCCACTCGTACAGCAGACCATTATGCTACCTCACAATAGTTCATAACAGTGACCATATTTCTCGAAGCTCCCCAACGAGCACCTCCATGCTCTGAGTGGCCACCCCCCGGCCCTGGTGCTTGCGGAGGGCAGGTCAACCGGCATGGGGCTACCGAAATCCCCGACCGGATCCCACCACCCCCGCGATGGGAAGAATCTCTCCCCGGGATGTGGGCCCACCACCAGCACAACCTGCTGGCCCAGGCGAGCGTCAAACCATACCACACAAATATCCTTGGCATCGGCCCTGAATTCCTTCTGCCGCTCTGCTACCCGGTGCTTCTGTCCGAAGCAGGGGTTGCTAGGGATCGCTCCGAGTCCGCAAACCCTTGTCGCGTGGCGGGGCTTGTTCGAGCTT gaagagc

The resulting strain was further transformed with a construct designedto recombine at (and thereby disrupt) the endogenous FATA and alsoexpress the LPAAT from B. napus under control of the UAPA1 promoter andusing alpha galactosidase as a selectable marker with selection onmelbiose. The resulting strain showed increased production of SOS (about57-60%) and Sat-O-Sat (about 70-76%) and lower amounts of trisaturates(4.8 to 7.6%).

Strains were generated in the high-C18:0 S6573 background in which wemaximized SOS production and minimized the formation of trisaturatedTAGs by targeting both the Brassica napus LPAT2(Bnl.13) gene and thePmFAD2hpA RNAi construct to the FATA-1 locus. The sequence of thetransforming DNA from the PmFAD2hpA expression construct pSZ4164 isshown below in SEQ ID NO:153. Relevant restriction sites are indicatedin lowercase, bold, and are from 5′-3′ BspQI, KpnI, SpeI, SnaBI, BamHI,NdeI, NsiI, AflII, EcoRI, SpeI, BsiWI, XhoI, SacI and BspQI. Underlinedsequences at the 5′ and 3′ flanks of the construct represent genomic DNAfrom P. moriformis that enable targeted integration of the transformingDNA via homologous recombination at the FATA-1 locus. Proceeding in the5′ to 3′ direction, the PmHXT1 promoter driving the expression ofSaccharomyces carlbergensis MEL1 (ScarMEL1) gene, enabling strains toutilize exogenous melibiose, is indicated by lowercase, boxed text. Theinitiator ATG and terminator TGA of ScarMEL1 are indicated by uppercaseitalics, while the coding region is represented by lowercase italics.The 3′ UTR of the P. moriformis PGK gene is indicated by small capitals.A spacer region is represented by lowercase text. The P. moriformisUAPA1 promoter driving the expression of the BnLPAT2(Bnl.13) gene isindicated by lowercase, boxed text. The initiator ATG and terminator TGAare indicated by uppercase italics; the sequence encodingBnLPAT2(Bnl.13) is represented by lowercase, underlined italics. The 3′UTR of the CvNR gene is indicated by small capitals. A second spacerregion is represented by lowercase text. The C. reinhardtii CrTUB2promoter driving the expression of the PmFAD2hpA hairpin sequence isindicated by lowercase, boxed text. The FAD2 exon 1 sequence in theforward orientation is indicated with lowercase italics; the FAD2 intron1 sequence is represented with lowercase, bold italics; a short linkerregion is indicated with lowercase text, and the FAD2 exon 1 sequence inthe reverse orientation is indicated with lowercase, underlined italics.A second CvNR 3′ UTR is indicated by small capitals.

Nucleotide sequence of the transforming DNA from pSZ4164:(SEQ ID NO: 153)gctcttcCCAACTCAGATAATACCAATACCCCTCCTTCTCCTCCTCATCCATTCAGTACCCCCCCCCTTCTCTTCCCAAAGCAGCAAGCGCGTGGCTTACAGAAGAACAATCGGCTTCCGCCAAAGTCGCCGAGCACTGCCCGACGGCGGCGCGCCCAGCAGCCCGCTTGGCCACACAGGCAACGAATACATTCAATAGGGGGCCTCGCAGAATGGAAGGAGCGGTAAAGGGTACAGGAGCACTGCGCACAAGGGGCCTGTGCAGGAGTGACTGACTGGGCGGGCAGACGGCGCACCGCGGGCGCAGGCAAGCAGGGAAGATTGAAGCGGCAGGGAGGAGGATGCTGATTGAGGGGGGCATCGCAGTCTCTCTTGGACCCGGGATAAGGAAGCAAATATTCGGCCGGTTGGGTTGTGTGTGTGCACGTTTTCTTCTTCAGAGTCGTGGGTGTGCTTCCAGGGAGGATATAAGCAGCAGGATCGAATCCCGCGACCAGCGTTTCCCCATCCAGCCAACCACCCTGTC ggtac

gtgttcggcgtctccccctcctacaacggcctgggcctgacgccccagatgggctgggacaactggaacacgttcgcctgcgacgtctccgagcagctgctgctggacacggccgaccgcatctccgacctgggcctgaaggacaatgggctacaagtacatcatcctggacgactgctggtcctccggccgcgactccgacggcttcctggtcgccgacgagcagaagttccccaacggcatgggccacgtcgccgaccacctgcacaacaactccttcctgttcggcatgtactcctccgcgggcgagtacacgtgcgccggctaccccggctccctgggccgcgaggaggaggacgcccagttcttcgcgaacaaccgcgtggactacctgaatacgacaactgctacaacaagggccagttcggcacgcccgagatctcctaccaccgctacaaggccatgtccgacgccctgaacaagacgggccgccccatcttctactccctgtgcaactggggccaggacctgaccttctactggggctccggcatcgcgaactcctggcgcatgtccggcgacgtcacggcggagttcacgcgccccgactcccgctgcccctgcgacggcgacgagtacgactgcaagtacgccggcttccactgctccatcatgaacatcctgaacaaggccgcccccatgggccagaacgcgggcgtcggcggctggaacgacctggacaacctggaggtcggcgtcggcaacctgacggacgacgaggagaaggcgcacttctccatgtgggccatggtgaagtcccccctgatcatcggcgcgaacgtgaacaacctgaaggcctcctcctactccatctgctcccaggcgtccgtcatcgccatcaaccaggactccaacggcatccccgccacgcgcgtctggcgctactacgtgtccgacacggacgagtacggccagggcgagatccagatgtggtccggccccctggacaacggcgaccaggtcgtggcgctgctgaacggcggctccgtgtcccgccccatgaacacgaccctggaggagatcttcttcgactccaacctgggctccaagaagctgacctccacctgggacatctacgacctgtgggcgaaccgcgtcgacaactcccacggcgtccgccatcctgggccgcaacaagaccgccaccggcatcctgtacaacgccaccgagcagtcctacaaggacggcctgtccaagaacgacacccgcctgttcggccagaagatcggctccctgtcccccaacgcgatcctgaacacgaccgtccccgcccacggcatcgcgttctaccgcctgcgcccctcctccTGAtacaacttattacgtaTTCTGACCGGCGCTGATGTGGCGCGGACGCCGTCGTACTCTTTCAGACTTTACTCTTGAGGAATTGAACCTTTCTCGCTTGCTGGCATGTAAACATTGGCGCAATTAATTGTGTGATGAAGAAAGGGTGGCACAAGATGGATCGCGAATGTACGAGATCGACAACGATGGTGATTGTTATGAGGGGCCAAACCTGGCTCAATCTTGTCGCATGTCCGGCGCAATGTGATCCAGCGGCGTGACTCTCGCAACCTGGTAGTGTGTGGCGCACCGGGTCGCTTTGATTAAAACTGATCGCATTGCCATCCCGTCAACTCACAAGCCTACTCTAGCTCCCATTGCGCACTCGGGCGCCCGGCTCGATCAATGTTCTGAGCGGAGGGCGAAGCGTCAGGAAATCGTCTCGGCAGCTGGAAGCGCATGGAATGCGGAGCGGAGATCGAATCAggatcccgcgtctcgaacagagcgcgcagaggaacgctgaaggtctcgcctctgtcgcacctcagcgcggcatacaccacaataaccacctgacgaatgcgcttggttcttcgtccattagcgaagcgtccggttcacacacgtgccacgttg

ctgctgcaggccatctgctacgtgctgatccgccccctgtccaagaacacctaccgcaagatcaaccgcgtggtggccgagaccctgtggctggagctggtgtggatcgtggactggtgggccggcgtgaagatccaggtgttcgccgacaacgagaccttcaaccgcatgggcaaggagcacgccctggtggtgtgcaaccaccgctccgacatcgactggctggtgggctggatcctggcccagcgctccggctgcctgggctccgccctggccgtgatgaagaagtcctccaagttcctgcccgtgatcggctggtccatgtggttctccgagtacctgttcctggagcgcaactgggccaaggacgagtccaccctgaagtccggcctgcagcgcctgaacgacttcccccgccccttctggctggccctgttcgtggagggcacccgcttcaccgaggccaagctgaaggccgcccaggagtacgccgcctcctccgagctgcccgtgccccgcaacgtgctgatcccccgcaccaagggcttcgtgtccgccgtgtccaacatgcgctccttcgtgcccgccatctacgacatgaccgtggccatccccaagacctcccccccccccaccatgctgcgcctgttcaagggccagccctccgtggtgcacgtgcacatcaagtgccactccatgaaggacctgcccgagtccgacgacgccatcgcccagtggtgccgcgaccagttcgtggccaaggacgccctgctggacaagcacatcgccgccgacaccttccccggccagcaggagcagaacatcggccgccccatcaagtccctggccgtggtgctgtcctggtcctgcctgctgatcctgggcgccatgaagttcctgactggtccaacctgttctcctcctggaagggcatcgccttctccgccctgggcctgggcatcatcaccctgtgcatgcagatcctgatccgctcctcccagtccgagcgctccacccccgccaggtggtgcccgccaagcccaaggacaaccacaacgactcggctcctcctcccagaccgaggtggagaagcagaagTGAatgcatGCAGCAGCAGCTCGGATGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGActtaaggatctaagtaagattcgaagcgctcgaccgtgccggacggactgcagccccatgtcgtagtgaccgccaatgtaagtgggctggcgtttccctgtacgtgagtcaacgtcactgcacgcgcaccaccctctcgaccggcaggaccaggcatcgcgagatacagcgcgagccagacacggagtgccgagctatgcgcacgctccaactagatatcatgtggatgatgagcatgaatt

gtggagaagcctccgttcacgatcgggacgctgcgcaaggccatccccgcgcactgtttcgagcgctcggcgcttcgtagcagcatgtacctggcctttgacatcgcggtcatgtccctgctctacgtcgcgtcgacgtacatcgaccctgcaccggtgcctacgtggg

agtagagcggccacatgatgccgtacttgacccacgtaggcaccggtgcagggtcgatatacgtcgacacgacatagggcagggacatgaccgcgatgtcaaaggccaggtacatgctgctacgaagcgccgagcactcgaaacggtacgcggggatggccttgcgcagcgtcccgatcgtgaacggaggcttctccacaggctgcctgttcgtcttgatagccatctcgagGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAAAGCTGTAgagctcttgttttccagaaggagttgctccttgagcctttcattctcagcctcgataacctccaaagccgctctaattgtggagggggttcgaaCCGAATGCTGCGTGAACGGGAAGGAGGAGGAGAAAGAGTGAGCAGGGAGGGATTCAGAAATGAGAAATGAGAGGTGAAGGAACGCATCCCTATGCCCTTGCAATGGACAGTGTTTCTGGCCACCGCCACCAAGACTTCGTGTCCTCTGATCATCATGCGATTGATTACGTTGAATGCGACGGCCGGTCAGCCCCGGACCTCCACGCACCGGTGCTCCTCCAGGAAGATGCGCTTGTCCTCCGCCATCTTGCAGGGCTCAAGCTGCTCCCAAAACTCTTGGGCGGGTTCCGGACGGACGGCTACCGCGGGTGCGGCCCTGACCGCCACTGTTCGGAAGCAGCGGCGCTGCATGGGCAGCGGCCGCTGCGGTGCGCCACGGACCGCATGATCCACCGGAAAAGCGCACGCGCTGGAGCGCGCAGAGGACCACAGAGAAGCGGAAGAGACGCCAGTACTGGCAAGCAGGCTGGTCGGTGCCATGGCGCGCTACTACCCTCGCTATGACTCGGGTCCTCGGCCGGCTGGCGGTGCTGACAATTCGTTTAGTGGAGCAGCGACTCCATTCAGCTACCAGTCGAACTCAGTGGCACAGTGACTccgctcttc

The described embodiments of the invention are intended to be merelyexemplary and numerous variations and modifications will be apparent tothose skilled in the art. All such variations and modifications areintended to be within the scope of the present invention. For example,the various triglyceride oils can be tailored in for a mixture ofmidchain and long chain fatty acids in order to adjust parameters suchas polarity, solvency, and foam-height of the oils or chemicals madefrom the oils. In addition, where a knockout of a gene is called for, anequivalent result may be reached using knockdown techniques includingmutation and expression of inhibitory substances such as RNAi orantisense.

SEQUENCE LISTING SEQ ID NO: 1 6S 5′ genomic donor sequenceGCTCTTCGCCGCCGCCACTCCTGCTCGAGCGCGCCCGCGCGTGCGCCGCCAGCGCCTTGGCCTTTTCGCCGCGCTCGTGCGCGTCGCTGATGTCCATCACCAGGTCCATGAGGTCTGCCTTGCGCCGGCTGAGCCACTGCTTCGTCCGGGCGGCCAAGAGGAGCATGAGGGAGGACTCCTGGTCCAGGGTCCTGACGTGGTCGCGGCTCTGGGAGCGGGCCAGCATCATCTGGCTCTGCCGCACCGAGGCCGCCTCCAACTGGTCCTCCAGCAGCCGCAGTCGCCGCCGACCCTGGCAGAGGAAGACAGGTGAGGGGGGTATGAATTGTACAGAACAACCACGAGCCTTGTCTAGGCAGAATCCCTACCAGTCATGGCTTTACCTGGATGACGGCCTGCGAACAGCTGTCCAGCGACCCTCGCTGCCGCCGCTTCTCCCGCACGCTTCTTTCCAGCACCGTGATGGCGCGAGCCAGCGCCGCACGCTGGCGCTGCGCTTCGCCGATCTGAGGACAGTCGGGGAACTCTGATCAGTCTAAACCCCCTTGCGCGTTAGTGTTGCCATCCTTTGCAGACCGGTGAGAGCCGACTTGTTGTGCGCCACCCCCCACACCACCTCCTCCCAGACCAATTCTGTCACCTTTTTGGCGAAGGCATCGGCCTCGGCCTGCAGAGAGGACAGCAGTGCCCAGCCGCTGGGGGTTGGCGGATGCACGCTCAGGTACC SEQ ID NO: 2 6S 3′genomic donor sequenceGAGCTCCTTGTTTTCCAGAAGGAGTTGCTCCTTGAGCCTTTCATTCTCAGCCTCGATAACCTCCAAAGCCGCTCTAATTGTGGAGGGGGTTCGAATTTAAAAGCTTGGAATGTTGGTTCGTGCGTCTGGAACAAGCCCAGACTTGTTGCTCACTGGGAAAAGGACCATCAGCTCCAAAAAACTTGCCGCTCAAACCGCGTACCTCTGCTTTCGCGCAATCTGCCCTGTTGAAATCGCCACCACATTCATATTGTGACGCTTGAGCAGTCTGTAATTGCCTCAGAATGTGGAATCATCTGCCCCCTGTGCGAGCCCATGCCAGGCATGTCGCGGGCGAGGACACCCGCCACTCGTACAGCAGACCATTATGCTACCTCACAATAGTTCATAACAGTGACCATATTTCTCGAAGCTCCCCAACGAGCACCTCCATGCTCTGAGTGGCCACCCCCCGGCCCTGGTGCTTGCGGAGGGCAGGTCAACCGGCATGGGGCTACCGAAATCCCCGACCGGATCCCACCACCCCCGCGATGGGAAGAATCTCTCCCCGGGATGTGGGCCCACCACCAGCACAACCTGCTGGCCCAGGCGAGCGTCAAACCATACCACACAAATATCCTTGGCATCGGCCCTGAATTCCTTCTGCCGCTCTGCTACCCGGTGCTTCTGTCCGAAGCAGGGGTTGCTAGGGATCGCTCCGAGTCCGCAAACCCTTGTCGCGTGGCGGGGCTTGTTCGAGCTTGAAGAG CSEQ ID NO: 3 S. cereviseae invertase protein sequenceMLLQAFLFLLAGFAAKISASMTNETSDRPLVHFTPNKGWMNDPNGLWYDEKDAKWHLYFQYNPNDTVWGTPLFWGHATSDDLTNWEDQPIAIAPKRNDSGAFSGSMVVDYNNTSGFFNDTIDPRQRCVAIWTYNTPESEEQYISYSLDGGYTFTEYQKNPVLAANSTQFRDPKVFWYEPSQKWIMTAAKSQDYKIETYSSDDLKSWKLESAFANEGFLGYQYECPGLIEVPTEQDPSKSYWVMFISINPGAPAGGSFNQYFVGSFNGTHFEAFDNQSRVVDFGKDYYALQTFFNTDPTYGSALGIAWASNWEYSAFVPTNPWRSSMSLVRKFSLNTEYQANPETELINLKAEPILNISNAGPWSRFATNTTLTKANSYNVDLSNSTGTLEFELVYAVNTTQTISKSVFADLSLWFKGLEDPEEYLRMGFEVSASSFFLDRGNSKVKFVKENPYFTNRMSVNNQPFKSENDLSYYKVYGLLDQNILELYFNDGDVVSTNTYFMTTGNALGSVNMTTGVDNLFYIDKFQVREVK SEQ ID NO: 4S. cereviseae invertase protein coding sequence codon optimized forexpression in P. moriformis (UTEX 1435)ATGctgctgcaggccttcctgttcctgctggccggcttcgccgccaagatcagcgcctccatgacgaacgagacgtccgaccgccccctggtgcacttcacccccaacaagggctggatgaacgaccccaacggcctgtggtacgacgagaaggacgccaagtggcacctgtacttccagtacaacccgaacgacaccgtctgggggacgcccttgttctggggccacgccacgtccgacgacctgaccaactgggaggaccagcccatcgccatcgccccgaagcgcaacgactccggcgccttctccggctccatggtggtggactacaacaacacctccggcttcttcaacgacaccatcgacccgcgccagcgctgcgtggccatctggacctacaacaccccggagtccgaggagcagtacatctcctacagcctggacggcggctacaccttcaccgagtaccagaagaaccccgtgctggccgccaactccacccagttccgcgacccgaaggtcttctggtacgagccctcccagaagtggatcatgaccgcggccaagtcccaggactacaagatcgagatctactcctccgacgacctgaagtcctggaagctggagtccgcgttcgccaacgagggcttcctcggctaccagtacgagtgccccggcctgatcgaggtccccaccgagcaggaccccagcaagtcctactgggtgatgttcatctccatcaaccccggcgccccggccggcggctccttcaaccagtacttcgtcggcagcttcaacggcacccacttcgaggccttcgacaaccagtcccgcgtggtggacttcggcaaggactactacgccctgcagaccttcttcaacaccgacccgacctacgggagcgccctgggcatcgcgtgggcctccaactgggagtactccgccttcgtgcccaccaacccctggcgctcctccatgtccctcgtgcgcaagttctccctcaacaccgagtaccaggccaacccggagacggagctgatcaacctgaaggccgagccgatcctgaacatcagcaacgccggcccctggagccggttcgccaccaacaccacgttgacgaaggccaacagctacaacgtcgacctgtccaacagcaccggcaccctggagttcgagctggtgtacgccgtcaacaccacccagacgatctccaagtccgtgttcgcggacctctccctctggttcaagggcctggaggaccccgaggagtacctccgcatgggcttcgaggtgtccgcgtcctccttcttcctggaccgcgggaacagcaaggtgaagttcgtgaaggagaacccctacttcaccaaccgcatgagcgtgaacaaccagcccttcaagagcgagaacgacctgtcctactacaaggtgtacggcttgctggaccagaacatcctggagctgtacttcaacgacggcgacgtcgtgtccaccaacacctacttcatgaccaccgggaacgccctgggctccgtgaacatgacgacgggggtggacaacctgttctacatcgacaagttccaggtgcgcgaggtcaagTGA SEQ ID NO: 5Chlamydomonas reinhardtii TUB2 (B-tub) promoter/5′ UTRCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAAC SEQ ID NO: 6Chlorella vulgaris nitrate reductase 3′UTRGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAAAGCTTSEQ ID NO: 7Nucleotide sequence of the codon-optimized expression cassette of S.cerevisiae suc2 gene with C. reinhardtii β-tubulin promoter/5′UTRand C. vulgaris nitrate reductase 3′ UTRCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACGGCGCGCCATGCTGCTGCAGGCCTTCCTGTTCCTGCTGGCCGGCTTCGCCGCCAAGATCAGCGCCTCCATGACGAACGAGACGTCCGACCGCCCCCTGGTGCACTTCACCCCCAACAAGGGCTGGATGAACGACCCCAACGGCCTGTGGTACGACGAGAAGGACGCCAAGTGGCACCTGTACTTCCAGTACAACCCGAACGACACCGTCTGGGGGACGCCCTTGTTCTGGGGCCACGCCACGTCCGACGACCTGACCAACTGGGAGGACCAGCCCATCGCCATCGCCCCGAAGCGCAACGACTCCGGCGCCTTCTCCGGCTCCATGGTGGTGGACTACAACAACACCTCCGGCTTCTTCAACGACACCATCGACCCGCGCCAGCGCTGCGTGGCCATCTGGACCTACAACACCCCGGAGTCCGAGGAGCAGTACATCTCCTACAGCCTGGACGGCGGCTACACCTTCACCGAGTACCAGAAGAACCCCGTGCTGGCCGCCAACTCCACCCAGTTCCGCGACCCGAAGGTCTTCTGGTACGAGCCCTCCCAGAAGTGGATCATGACCGCGGCCAAGTCCCAGGACTACAAGATCGAGATCTACTCCTCCGACGACCTGAAGTCCTGGAAGCTGGAGTCCGCGTTCGCCAACGAGGGCTTCCTCGGCTACCAGTACGAGTGCCCCGGCCTGATCGAGGTCCCCACCGAGCAGGACCCCAGCAAGTCCTACTGGGTGATGTTCATCTCCATCAACCCCGGCGCCCCGGCCGGCGGCTCCTTCAACCAGTACTTCGTCGGCAGCTTCAACGGCACCCACTTCGAGGCCTTCGACAACCAGTCCCGCGTGGTGGACTTCGGCAAGGACTACTACGCCCTGCAGACCTTCTTCAACACCGACCCGACCTACGGGAGCGCCCTGGGCATCGCGTGGGCCTCCAACTGGGAGTACTCCGCCTTCGTGCCCACCAACCCCTGGCGCTCCTCCATGTCCCTCGTGCGCAAGTTCTCCCTCAACACCGAGTACCAGGCCAACCCGGAGACGGAGCTGATCAACCTGAAGGCCGAGCCGATCCTGAACATCAGCAACGCCGGCCCCTGGAGCCGGTTCGCCACCAACACCACGTTGACGAAGGCCAACAGCTACAACGTCGACCTGTCCAACAGCACCGGCACCCTGGAGTTCGAGCTGGTGTACGCCGTCAACACCACCCAGACGATCTCCAAGTCCGTGTTCGCGGACCTCTCCCTCTGGTTCAAGGGCCTGGAGGACCCCGAGGAGTACCTCCGCATGGGCTTCGAGGTGTCCGCGTCCTCCTTCTTCCTGGACCGCGGGAACAGCAAGGTGAAGTTCGTGAAGGAGAACCCCTACTTCACCAACCGCATGAGCGTGAACAACCAGCCCTTCAAGAGCGAGAACGACCTGTCCTACTACAAGGTGTACGGCTTGCTGGACCAGAACATCCTGGAGCTGTACTTCAACGACGGCGACGTCGTGTCCACCAACACCTACTTCATGACCACCGGGAACGCCCTGGGCTCCGTGAACATGACGACGGGGGTGGACAACCTGTTCTACATCGACAAGTTCCAGGTGCGCGAGGTCAAGTGACAATTGGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCIGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAGGATCC SEQ ID NO: 8Prototheca moriformis (UTEX 435) Amt03 promoterGGCCGACAGGACGCGCGTCAAAGGTGCTGGTCGTGTATGCCCTGGCCGGCAGGTCGTTGCTGCTGCTGGTTAGTGATTCCGCAACCCTGATTTTGGCGTCTTATTTTGGCGTGGCAAACGCTGGCGCCCGCGAGCCGGGCCGGCGGCGATGCGGTGCCCCACGGCTGCCGGAATCCAAGGGAGGCAAGAGCGCCCGGGTCAGTTGAAGGGCTTTACGCGCAAGGTACAGCCGCTCCTGCAAGGCTGCGTGGTGGAATTGGACGTGCAGGTCCTGCTGAAGTTCCTCCACCGCCTCACCAGCGGACAAAGCACCGGTGTATCAGGTCCGTGTCATCCACTCTAAAGAGCTCGACTACGACCTACTGATGGCCCTAGATTCTTCATCAAAAACGCCTGAGACACTTGCCCAGGATTGAAACTCCCTGAAGGGACCACCAGGGGCCCTGAGTTGTTCCTTCCCCCCGTGGCGAGCTGCCAGCCAGGCTGTACCTGTGATCGAGGCTGGCGGGAAAATAGGCTTCGTGTGCTCAGGTCATGGGAGGTGCAGGACAGCTCATGAAACGCCAACAATCGCACAATTCATGTCAAGCTAATCAGCTATTTCCTCTTCACGAGCTGTAATTGTCCCAAAATTCTGGTCTACCGGGGGTGATCCTTCGTGTACGGGCCCTTCCCTCAACCCTAGGTATGCGCGCATGCGGTCGCCGCGCAACTCGCGCGAGGGCCGAGGGTTTGGGACGGGCCGTCCCGAAATGCAGTTGCACCCGGATGCGTGGCACCTTTTTTGCGATAATTTATGCAATGGACTGCTCTGCAAAATTCTGGCTCTGTCGCCAACCCTAGGATCAGCGGCGTAGGATTTCGTAATCATTCGTCCTGATGGGGAGCTACCGACTACCCTAATATCAGCCCGACTGCCTGACGCCAGCGTCCACTTTTGTGCACACATTCCATTCGTGCCCAAGACATTTCATTGTGGTGCGAAGCGTCCCCAGTTACGCTCACCTGTTTCCCGACCTCCTTACTGTTCTGTCGACAGAGCGGGCCCACAGGCCGGTCGCAGCC SEQ ID NO: 9Chlorella protothecoides (UTEX 250) stearoyl ACP desaturase transitpeptide cDNA sequence codon optimized for expression in P. moriformis.ACTAGTATGGCCACCGCATCCACTTTCTCGGCGTTCAATGCCCGCTGCGGCGACCTGCGTCGCTCGGCGGGCTCCGGGCCCCGGCGCCCAGCGAGGCCCCTCCCCGTGCGCGGGCGCGCC SEQ ID NO: 10Cuphea wrightii FatB2 thioesterase nucleic acid sequence; Gen BankAccession No. U56104ATGGTGGTGGCCGCCGCCGCCAGCAGCGCCTTCTTCCCCGTGCCCGCCCCCCGCCCCACCCCCAAGCCCGGCAAGTTCGGCAACTGGCCCAGCAGCCTGAGCCAGCCCTTCAAGCCCAAGAGCAACCCCAACGGCCGCTTCCAGGTGAAGGCCAACGTGAGCCCCCACGGGCGCGCCCCCAAGGCCAACGGCAGCGCCGTGAGCCTGAAGTCCGGCAGCCTGAACACCCTGGAGGACCCCCCCAGCAGCCCCCCCCCCCGCACCTTCCTGAACCAGCTGCCCGACTGGAGCCGCCTGCGCACCGCCATCACCACCGTGTTCGTGGCCGCCGAGAAGCAGTTCACCCGCCTGGACCGCAAGAGCAAGCGCCCCGACATGCTGGTGGACTGGTTCGGCAGCGAGACCATCGTGCAGGACGGCCTGGTGTTCCGCGAGCGCTTCAGCATCCGCAGCTACGAGATCGGCGCCGACCGCACCGCCAGCATCGAGACCCTGATGAACCACCTGCAGGACACCAGCCTGAACCACTGCAAGAGCGTGGGCCTGCTGAACGACGGCTTCGGCCGCACCCCCGAGATGTGCACCCGCGACCTGATCTGGGTGCTGACCAAGATGCAGATCGTGGTGAACCGCTACCCCACCTGGGGCGACACCGTGGAGATCAACAGCTGGTTCAGCCAGAGCGGCAAGATCGGCATGGGCCGCGAGTGGCTGATCAGCGACTGCAACACCGGCGAGATCCTGGTGCGCGCCACCAGCGCCTGGGCCATGATGAACCAGAAGACCCGCCGCTTCAGCAAGCTGCCCTGCGAGGTGCGCCAGGAGATCGCCCCCCACTTCGTGGACGCCCCCCCCGTGATCGAGGACAACGACCGCAAGCTGCACAAGTTCGACGTGAAGACCGGCGACAGCATCTGCAAGGGCCTGACCCCCGGCTGGAACGACTTCGACGTGAACCAGCACGTGAGCAACGTGAAGTACATCGGCTGGATTCTGGAGAGCATGCCCACCGAGGTGCTGGAGACCCAGGAGCTGTGCAGCCTGACCCTGGAGTACCGCCGCGAGTGCGGCCGCGAGAGCGTGGTGGAGAGCGTGACCAGCATGAACCCCAGCAAGGTGGGCGACCGCAGCCAGTACCAGCACCTGCTGCGCCTGGAGGACGGCGCCGACATCATGAAGGGCCGCACCGAGTGGCGCCCCAAGAACGCCGGCACCAACCGCGCCATCAGCACCTGA SEQ ID NO: 11Cuphea wrightii FatB2 thioesterase amino acid sequence; Gen BankAccession No. U56104MVVAAAASSAFFPVPAPRPTPKPGKFGNWPSSLSQPFKPKSNPNGRFQVKANVSPHPKANGSAVSLKSGSLNTLEDPPSSPPPRTFLNQLPDWSRLRTAITTVFVAAEKQFTRLDRKSKRPDMLVDWFGSETIVQDGLVFRERFSIRSYEIGADRTASIETLMNHLQDTSLNHCKSVGLLNDGFGRTPEMCTRDLIWVLTKMQIVVNRYPTWGDIVEINSWFSQSGKIGMGREWLISDCNTGEILVRATSAWAMMNQKTRRESKLPCEVRQEIAPHFVDAPPVIEDNDRKLHKFDVKTGDSICKGLTPGWNDFDVNQHVSNVKYIGWILESMPTEVLETQELCSLTLEYRRECGRESVVESVTSMNPSKVGDRSQYQHLLRLEDGADIMKGRTEWRPKNAGTNRAISTSEQ ID NO: 12Codon-optimized coding region of Cocus nucifera C12:0-preferringLPAAT from pSZ2046ATGGACGCCTCCGGCGCCTCCTCCTTCCTGCGCGGCCGCTGCCTGGAGTCCTGCTTCAAGGCCTCCTTCGGCTACGTAATGTCCCAGCCCAAGGACGCCGCCGGCCAGCCCTCCCGCCGCCCCGCCGACGCCGACGACTTCGTGGACGACGACCGCTGGATCACCGTGATCCTGTCCGTGGTGCGCATCGCCGCCTGCTTCCTGTCCATGATGGTGACCACCATCGTGTGGAACATGATCATGCTGATCCTGCTGCCCTGGCCCTACGCCCGCATCCGCCAGGGCAACCTGTACGGCCACGTGACCGGCCGCATGCTGATGTGGATTCTGGGCAACCCCATCACCATCGAGGGCTCCGAGTTCTCCAACACCCGCGCCATCTACATCTGCAACCACGCCTCCCTGGTGGACATCTTCCTGATCATGTGGCTGATCCCCAAGGGCACCGTGACCATCGCCAAGAAGGAGATCATCTGGTATCCCCTGTTCGGCCAGCTGTACGTGCTGGCCAACCACCAGCGCATCGACCGCTCCAACCCCTCCGCCGCCATCGAGTCCATCAAGGAGGTGGCCCGCGCCGTGGTGAAGAAGAACCTGTCCCTGATCATCTTCCCCGAGGGCACCCGCTCCAAGACCGGCCGCCTGCTGCCCTTCAAGAAGGGCTTCATCCACATCGCCCTCCAGACCCGCCTGCCCATCGTGCCGATGGTGCTGACCGGCACCCACCTGGCCTGGCGCAAGAACTCCCTGCGCGTGCGCCCCGCCCCCATCACCGTGAAGTACTTCTCCCCCATCAAGACCGACGACTGGGAGGAGGAGAAGATCAACCACTACGTGGAGATGATCCACGCCCTGTACGTGGACCACCTGCCCGAGTCCCAGAAGCCCCTGGTGTCCAAGGGCCGCGACGCCTCCGGCCGCTCCAACTCCTGA SEQ ID NO: 13 pLoop 5′genomic donor sequencegctcttcgctaacggaggtctgtcaccaaatggaccccgtctattgcgggaaaccacggcgatggcacgtttcaaaacttgatgaaatacaatattcagtatgtcgcgggcggcgacggcggggagctgatgtcgcgctgggtattgcttaatcgccagcttcgcccccgtcttggcgcgaggcgtgaacaagccgaccgatgtgcacgagcaaatcctgacactagaagggctgactcgcccggcacggctgaattacacaggcttgcaaaaataccagaatttgcacgcaccgtattcgcggtattttgttggacagtgaatagcgatgcggcaatggcttgtggcgttagaaggtgcgacgaaggtggtgccaccactgtgccagccagtcctggcggctcccagggccccgatcaagagccaggacatccaaactacccacagcatcaacgccccggcctatactcgaaccccacttgcactctgcaatggtatgggaaccacggggcagtcttgtgtgggtcgcgcctatcgcggtcggcgaagaccgggaaggtacc SEQ ID NO: 14 pLoop 3′ genomic donor sequencegagctcagcggcgacggtcctgctaccgtacgacgttgggcacgcccatgaaagtttgtataccgagcttgttgagcgaactgcaagcgcggctcaaggatacttgaactcctggattgatatcggtccaataatggatggaaaatccgaacctcgtgcaagaactgagcaaacctcgttacatggatgcacagtcgccagtccaatgaacattgaagtgagcgaactgttcgcttcggtggcagtactactcaaagaatgagctgctgttaaaaatgcactctcgttctctcaagtgagtggcagatgagtgctcacgccttgcacttcgctgcccgtgtcatgccctgcgccccaaaatttgaaaaaagggatgagattattgggcaatggacgacgtcgtcgctccgggagtcaggaccggcggaaaataagaggcaacacactccgcttcttagctcttcc SEQ ID NO: 15NeoR expression cassette including C. reinhardtii p-tubulinpromoter/5′UTR and C. vulgaris nitrate reductase 3′ UTR

gcctccacgccggctcccccgccgcctgggtggagcgcctgttcggctacgactgggcccagcagaccatcggctgctccgacgccgccgtgttccgcctgtccgcccagggccgccccgtgctgttcgtgaagaccgacctgtccggcgccctgaacgagctgcaggacgaggccgcccgcctgtcctggctggccaccaccggcgtgccctgcgccgccgtgctggacgtggtgaccgaggccggccgcgactggctgctgctgggcgaggtgcccggccaggacctgctgtcctcccacctggcccccgccgagaaggtgtccatcatggccgacgccatgcgccgcctgcacaccctggaccccgccacctgccccttcgaccaccaggccaagcaccgcatcgagcgcgcccgcacccgcatggaggccggcctggtggaccaggacgacctggacgaggagcaccagggcctggcccccgccgagctgttcgcccgcctgaaggcccgcatgcccgacggcgaggacctggtggtgacccacggcgacgcctgcctgcccaacatcatggtggagaacggccgcttctccggcttcatcgactgcggccgcctgggcgtggccgaccgctaccaggacatcgccctggccacccgcgacatcgccgaggagctgggcggcgagtgggccgaccgcttcctggtgctgtacggcatcgccgcccccgactcccagcgcatcgccttctaccgcctgctggacgagttcttcTGA caattggcagcagcagctoggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatcc SEQ ID NO: 16Cocos nucifera 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT)MDASGASSFLRGRCLESCFKASFGYVMSQPKDAAGQPSRRPADADDFVDDDRWITVILSVVRIAACFLSMMVITIVWNMIMLILLPWPYARIRQGNLYGHVTGRMLMWILGNPITIEGSEFSNTRAIYICNHASLVDIFLIMMLIPKGIVTIAKKEIIWYPLFGQLYVLANHQRIDRSNPSAAIESIKEVARAVVKKNLSLIIFPEGTRSKTGRLLPFKKGFIHIALQTRLPIVPMVLTGTHLAWRKNSLRVRPAPITVKYFSPIKTDDWEEEKINHYVEMIHALYVDHLPESQKPLVSK GRDASGRSNSSEQ ID NO: 17 pSZ1500GGGCTGGTCTGAATCCTTCAGGCGGGTGTTACCCGAGAAAGAAAGGGTGCCGATTTCAAAGCAGACCCATGTGCCGGGCCCTGTGGCCTGTGTTGGCGCCTATGTAGTCACCCCCCCTCACCCAATTGTCGCCAGTTTGCGCACTCCATAAACTCAAAACAGCAGCTTCTGAGCTGCGCTGTTCAAGAACACCTCTGGGGTTTGCTCACCCGCGAGGTCGACGCCCAGCATGGCTATCAAGACGAACAGGCAGCCTGTGGAGAAGCCTCCGTTCACGATCGGGACGCTGCGCAAGGCCATCCCCGCGCACTGTTTCGAGCGCTCGGCGCTTCGTAGCAGCATGTACCTGGCCTTTGACATCGCGGTCATGTCCCTGCTCTACGTCGCGTCGACGTACATCGACCCTGCACCGGTGCCTACGTGGGTCAAGTACGGCATCATGTGGCCGCTCTACTGGTTCTTCCAGGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGAGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCCTTCGGCACGGGTGTCTGGGTGTGCGCGCACGAGTGCGGCCACCAGGCCTTTTCCTCCAGCCAGGCCATCAACGACGGCGTGGGCCTGGTGTTCCACAGCCTGCTGCTGGTGCCCTACTACTCCTGGAAGCACTCGCACCGGGTACCCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACTCTAGAATATCAATGCTGCTGCAGGCCTTCCTGTTCCTGCTGGCCGGCTTCGCCGCCAAGATCAGCGCCTCCATGACGAACGAGACGTCCGACCGCCCCCTGGTGCACTTCACCCCCAACAAGGGCTGGATGAACGACCCCAACGGCCTGTGGTACGACGAGAAGGACGCCAAGTGGCACCTGTACTTCCAGTACAACCCGAACGACACCGTCTGGGGGACGCCCTTGTTCTGGGGCCACGCCACGTCCGACGACCTGACCAACTGGGAGGACCAGCCCATCGCCATCGCCCCGAAGCGCAACGACTCCGGCGCCTTCTCCGGCTCCATGGTGGTGGACTACAACAACACCTCCGGCTTCTTCAACGACACCATCGACCCGCGCCAGCGCTGCGTGGCCATCTGGACCTACAACACCCCGGAGTCCGAGGAGCAGTACATCTCCTACAGCCTGGACGGCGGCTACACCTTCACCGAGTACCAGAAGAACCCCGTGCTGGCCGCCAACTCCACCCAGTTCCGCGACCCGAAGGTCTTCTGGTACGAGCCCTCCCAGAAGTGGATCATGACCGCGGCCAAGTCCCAGGACTACAAGATCGAGATCTACTCCTCCGACGACCTGAAGTCCTGGAAGCTGGAGTCCGCGTTCGCCAACGAGGGCTTCCTCGGCTACCAGTACGAGTGCCCCGGCCTGATCGAGGTCCCCACCGAGCAGGACCCCAGCAAGTCCTACTGGGTGATGTTCATCTCCATCAACCCCGGCGCCCCGGCCGGCGGCTCCTTCAACCAGTACTTCGTCGGCAGCTTCAACGGCACCCACTTCGAGGCCTTCGACAACCAGTCCCGCGTGGTGGACTTCGGCAAGGACTACTACGCCCTGCAGACCTTCTTCAACACCGACCCGACCTACGGGAGCGCCCTGGGCATCGCGTGGGCCTCCAACTGGGAGTACTCCGCCTTCGTGCCCACCAACCCCTGGCGCTCCTCCATGTCCCTCGTGCGCAAGTTCTCCCTCAACACCGAGTACCAGGCCAACCCGGAGACGGAGCTGATCAACCTGAAGGCCGAGCCGATCCTGAACATCAGCAACGCCGGCCCCTGGAGCCGGTTCGCCACCAACACCACGTTGACGAAGGCCAACAGCTACAACGTCGACCTGTCCAACAGCACCGGCACCCTGGAGTTCGAGCTGGTGTACGCCGTCAACACCACCCAGACGATCTCCAAGTCCGTGTTCGCGGACCTCTCCCTCTGGTTCAAGGGCCTGGAGGACCCCGAGGAGTACCTCCGCATGGGCTTCGAGGTGTCCGCGTCCTCCTTCTTCCTGGACCGCGGGAACAGCAAGGTGAAGTTCGTGAAGGAGAACCCCTACTTCACCAACCGCATGAGCGTGAACAACCAGCCCTTCAAGAGCGAGAACGACCTGTCCTACTACAAGGTGTACGGCTTGCTGGACCAGAACATCCTGGAGCTGTACTTCAACGACGGCGACGTCGTGTCCACCAACACCTACTTCATGACCACCGGGAACGCCCTGGGCTCCGTGAACATGACGACGGGGGTGGACAACCTGTTCTACATCGACAAGTTCCAGGTGCGCGAGGTCAAGTGACAATTGGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAGGATCCCGCGTCTCGAACAGAGCGCGCAGAGGAACGCTGAAGGTCTCGCCTCTGTCGCACCTCAGCGCGGCATACACCACAATAACCACCTGACGAATGCGCTTGGTTCTTCGTCCATTAGCGAAGCGTCCGGTTCACACACGTGCCACGTTGGCGAGGTGGCAGGTGACAATGATCGGTGGAGCTGATGGTCGAAACGTTCACAGCCTAGGGATATCGAATTCGGCCGACAGGACGCGCGTCAAAGGTGCTGGTCGTGTATGCCCTGGCCGGCAGGTCGTTGCTGCTGCTGGTTAGTGATTCCGCAACCCTGATTTTGGCGTCTTATTTTGGCGTGGCAAACGCTGGCGCCCGCGAGCCGGGCCGGCGGCGATGCGGTGCCCCACGGCTGCCGGAATCCAAGGGAGGCAAGAGCGCCCGGGTCAGTTGAAGGGCTTTACGCGCAAGGTACAGCCGCTCCTGCAAGGCTGCGTGGTGGAATTGGACGTGCAGGTCCTGCTGAAGTTCCTCCACCGCCTCACCAGCGGACAAAGCACCGGTGTATCAGGTCCGTGTCATCCACTCTAAAGAACTCGACTACGACCTACTGATGGCCCTAGATTCTTCATCAAAAACGCCTGAGACACTTGCCCAGGATTGAAACTCCCTGAAGGGACCACCAGGGGCCCTGAGTTGTTCCTTCCCCCCGTGGCGAGCTGCCAGCCAGGCTGTACCTGTGATCGAGGCTGGCGGGAAAATAGGCTTCGTGTGCTCAGGTCATGGGAGGTGCAGGACAGCTCATGAAACGCCAACAATCGCACAATTCATGTCAAGCTAATCAGCTATTTCCTCTTCACGAGCTGTAATTGTCCCAAAATTCTGGTCTACCGGGGGTGATCCTTCGTGTACGGGCCCTTCCCTCAACCCTAGGTATGCGCGCATGCGGTCGCCGCGCAACTCGCGCGAGGGCCGAGGGTTTGGGACGGGCCGTCCCGAAATGCAGTTGCACCCGGATGCGTGGCACCTTTTTTGCGATAATTTATGCAATGGACTGCTCTGCAAAATTCTGGCTCTGTCGCCAACCCTAGGATCAGCGGCGTAGGATTTCGTAATCATTCGTCCTGATGGGGAGCTACCGACTACCCTAATATCAGCCCGACTGCCTGACGCCAGCGTCCACTTTIGTGCACACATTCCATTCGTGCCCAAGACATTTCATTGTGGTGCGAAGCGTCCCCAGTTACGCTCACCTGTTTCCCGACCTCCTTACTGTTCTGTCGACAGAGCGGGCCCACAGGCCGGTCGCAGCCACTAGTATGGCCACCGCATCCACTTTCTCGGCGTTCAATGCCCGCTGCGGCGACCTGCGTCGCTCGGCGGGCTCCGGGCCCCGGCGCCCAGCGAGGCCCCTCCCCGTGCGCGGGCGCGCCGCCACCGGCGAGCAGCCCTCCGGCGTGGCCTCCCTGCGCGAGGCCGACAAGGAGAAGTCCCTGGGCAACCGCCTGCGCCTGGGCTCCCTGACCGAGGACGGCCTGTCCTACAAGGAGAAGTTCGTGATCCGCTGCTACGAGGTGGGCATCAACAAGACCGCCACCATCGAGACCATCGCCAACCTGCTGCAGGAGGTGGGCGGCAACCACGCCCAGGGCGTGGGCTTCTCCACCGACGGCTTCGCCACCACCACCACCATGCGCAAGCTGCACCTGATCTGGGTGACCGCCCGCATGCACATCGAGATCTACCGCTACCCCGCCTGGTCCGACGTGATCGAGATCGAGACCTGGGTGCAGGGCGAGGGCAAGGTGGGCACCCGCCGCGACTGGATCCTGAAGGACTACGCCAACGGCGAGGTGATCGGCCGCGCCACCTCCAAGTGGGTGATGATGAACGAGGACACCCGCCGCCTGCAGAAGGTGTCCGACGACGTGCGCGAGGAGTACCTGGTGTTCTGCCCCCGCACCCTGCGCCTGGCCTTCCCCGAGGAGAACAACAACTCCATGAAGAAGATCCCCAAGCTGGAGGACCCCGCCGAGTACTCCCGCCTGGGCCTGGTGCCCCGCCGCTCCGACCTGGACATGAACAAGCACGTGAACAACGTGACCTACATCGGCTGGGCCCTGGAGTCCATCCCCCCCGAGATCATCGACACCCACGAGCTGCAGGCCATCACCCTGGACTACCGCCGCGAGTGCCAGCGCGACGACATCGTGGACTCCCTGACCTCCCGCGAGCCCCTGGGCAACGCCGCCGGCGTGAAGTTCAAGGAGATCAACGGCTCCGTGTCCCCCAAGAAGGACGAGCAGGACCTGTCCCGCTTCATGCACCTGCTGCGCTCCGCCGGCTCCGGCCTGGAGATCAACCGCTGCCGCACCGAGTGGCGCAAGAAGCCCGCCAAGCGCATGGACTACAAGGACCACGACGGCGACTACAAGGACCACGACATCGACTACAAGGACGACGACGACAAGTGAATCGATAGATCTCTTAAGGCAGCAGCAGCTCGGATAGTATCGACACACTCTGGACGCTGGTCGTGTGATGGACTGTTGCCGCCACACTTGCTGCCTTGACCTGTGAATATCCCTGCCGCTTTTATCAAACAGCCTCAGTGTGTTTGATCTTGTGTGTACGCGCTTTTGCGAGTTGCTAGCTGCTTGTGCTATTTGCGAATACCACCCCCAGCATCCCCTTCCCTCGTTTCATATCGCTTGCATCCCAACCGCAACTTATCTACGCTGTCCTGCTATCCCTCAGCGCTGCTCCTGCTCCTGCTCACTGCCCCTCGCACAGCCTTGGTTTGGGCTCCGCCTGTATTCTCCTGGTACTGCAACCTGTAAACCAGCACTGCAATGCTGATGCACGGGAAGTAGTGGGATGGGAACACAAATGGAAAGCTTAATTAAGAGCTCCCGCCACCACTCCAACACGGGGTGCCTGGACAAGGACGAGGTGTTTGTGCCGCCGCACCGCGCAGTGGCGCACGAGGGCCTGGAGTGGGAGGAGTGGCTGCCCATCCGCATGGGCAAGGTGCTGGTCACCCTGACCCTGGGCTGGCCGCTGTACCTCATGTTCAACGTCGCCTCGCGGCCGTACCCGCGCTTCGCCAACCACTTTGACCCGTGGTCGCCCATCTTCAGCAAGCGCGAGCGCATCGAGGTGGTCATCTCCGACCTGGCGCTGGTGGCGGTGCTCAGCGGGCTCAGCGTGCTGGGCCGCACCATGGGCTGGGCCTGGCTGGTCAAGACCTACGTGGTGCCCTACCTGATCGTGAACATGTGGCTCGTGCTCATCACGCTGCTCCAGCACACGCACCCGGCGCTGCCGCACTACTTCGAGAAGGACTGGGACTGGCTGCGCGGCGCCATGGCCACCGTGGACCGCTCCATGGGCCCGCCCTTCATGGACAACATCCTGCACCACATCTCCGACACCCACGTGCTGCACCACCTCTTCAGCACCATCCCGCACTACCACGCCGAGGAGGCCTCCGCCGCCATCAGGCCCATCCTGGGCAAGTACTACCAGTCCGACAGCCGCTGGGTCGGCCGCGCCCTGTGGGAGGACTGGCGCGACTGCCGCTACGTCGTCCCGGACGCGCCCGAGGACGACTCCGCGCTCTGGTTCCACAAGTGAGTGAGTGA SEQ ID NO: 18 5′ FADc genomic region donor DNAGGGCTGGTCTGAATCCTTCAGGCGGGTGTTACCCGAGAAAGAAAGGGTGCCGATTTCAAAGCAGACCCATGTGCCGGGCCCTGTGGCCTGTGTTGGCGCCTATGTAGTCACCCCCCCTCACCCAATTGTCGCCAGTTTGCGCACTCCATAAACTCAAAACAGCAGCTTCTGAGCTGCGCTGTTCAAGAACACCTCTGGGGTTTGCTCACCCGCGAGGTCGACGCCCAGCATGGCTATCAAGACGAACAGGCAGCCTGTGGAGAAGCCTCCGTTCACGATCGGGACGCTGCGCAAGGCCATCCCCGCGCACTGTTTCGAGCGCTCGGCGCTTCGTAGCAGCATGTACCTGGCCTTTGACATCGCGGTCATGTCCCTGCTCTACGTCGCGTCGACGTACATCGACCCTGCACCGGTGCCTACGTGGGTCAAGTACGGCATCATGTGGCCGCTCTACTGGTTCTTCCAGGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGAGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCCTTCGGCACGGGTGTCTGGGTGTGCGCGCACGAGTGCGGCCACCAGGCCTTTTCCTCCAGCCAGGCCATCAACGACGGCGTGGGCCTGGTGTTCCACAGCCTGCTGCTGGTGCCCTACTACTCCTGGAAGCACTCGCACCG SEQ ID NO: 19 3′FADc genomic region donor DNACCGCCACCACTCCAACACGGGGTGCCTGGACAAGGACGAGGTGTTTGTGCCGCCGCACCGCGCAGTGGCGCACGAGGGCCTGGAGTGGGAGGAGTGGCTGCCCATCCGCATGGGCAAGGTGCTGGTCACCCTGACCCIGGGCTGGCCGCTGTACCTCATGTTCAACGTCGCCTCGCGGCCGTACCCGCGCTTCGCCAACCACTTTGACCCGTGGTCGCCCATCTTCAGCAAGCGCGAGCGCATCGAGGTGGTCATCTCCGACCTGGCGCTGGTGGCGGTGCTCAGCGGGCTCAGCGTGCTGGGCCGCACCATGGGCTGGGCCTGGCTGGTCAAGACCTACGTGGTGCCCTACCTGATCGTGAACATGTGGCTCGTGCTCATCACGCTGCTCCAGCACACGCACCCGGCGCTGCCGCACTACTTCGAGAAGGACTGGGACTGGCTGCGCGGCGCCATGGCCACCGTGGACCGCTCCATGGGCCCGCCCTTCATGGACAACATCCTGCACCACATCTCCGACACCCACGTGCTGCACCACCTCTTCAGCACCATCCCGCACTACCACGCCGAGGAGGCCTCCGCCGCCATCAGGCCCATCCTGGGCAAGTACTACCAGTCCGACAGCCGCTGGGTCGGCCGCGCCCTGTGGGAGGACTGGCGCGACTGCCGCTACGTCGTCCCGGACGCGCCCGAGGACGACTCCGCGCTCTGGTTCCACAAGTGAGTGAGTGA SEQ ID NO: 20 5′donor DNA sequence of Prototheca moriformis FATA1 knockouthomologous recombination targeting constructGCTCTTCGGAGTCACTGTGCCACTGAGTTCGACTGGTAGCTGAATGGAGTCGCTGCTCCACTAAACGAATTGTCAGCACCGCCAGCCGGCCGAGGACCCGAGTCATAGCGAGGGTAGTAGCGCGCCATGGCACCGACCAGCCTGCTTGCCAGTACTGGCGTCTCTTCCGCTTCTCTGTGGTCCTCTGCGCGCTCCAGCGCGTGCGCTTTTCCGGTGGATCATGCGGTCCGTGGCGCACCGCAGCGGCCGCTGCCCATGCAGCGCCGCTGCTTCCGAACAGTGGCGGTCAGGGCCGCACCCGCGGTAGCCGTCCGTCCGGAACCCGCCCAAGAGTTTTGGGAGCAGCTTGAGCCCTGCAAGATGGCGGAGGACAAGCGCATCTTCCTGGAGGAGCACCGGTGCGTGGAGGTCCGGGGCTGACCGGCCGTCGCATTCAACGTAATCAATCGCATGATGATCAGAGGACACGAAGTCTTGGTGGCGGTGGCCAGAAACACTGTCCATTGCAAGGGCATAGGGATGCGTTCCTTCACCTCTCATTTCTCATTTCTGAATCCCTCCCTGCTCACTCTTTCTCCTCCTCCTTCCCGTTCACGCAGCATTCGGGGTACCSEQ ID NO: 21 3′donor DNA sequence of Prototheca moriformis FATA1 knockouthomologous recombination targeting constructGACAGGGTGGTTGGCTGGATGGGGAAACGCTGGTCGCGGGATTCGATCCTGCTGCTTATATCCICCCTGGAAGCACACCCACGACTCTGAAGAAGAAAACGTGCACACACACAACCCAACCGGCCGAATATTTGCTTCCTTATCCCGGGTCCAAGAGAGACTGCGATGCCCCCCTCAATCAGCATCCTCCTCCCTGCCGCTTCAATCTTCCCTGCTTGCCTGCGCCCGCGGTGCGCCGTCTGCCCGCCCAGTCAGTCACTCCTGCACAGGCCCCTTGTGCGCAGTGCTCCTGTACCCTTTACCGCTCCTTCCATTCTGCGAGGCCCCCTATTGAATGTATTCGTTGCCTGTGTGGCCAAGCGGGCTGCTGGGCGCGCCGCCGTCGGGCAGTGCTCGGCGACTTTGGCGGAAGCCGATTGTTCTTCTGTAAGCCACGCGCTTGCTGCTTTGGGAAGAGAAGGGGGGGGGTACTGAATGGATGAGGAGGAGAAGGAGGGGTATTGGTATTATCTGAGTTGGGTGAAGAGC SEQ ID NO: 22Chlorella protothecoides actin promoter/5′UTRagtttaggtccagcgtccgtggggggggacgggctgggagcttgggccgggaagggcaagacgatgcagtccctctggggagtcacagccgactgtgtgtgttgcactgtgcggcccgcagcactcacacgcaaaatgcctggccgacaggcaggccctgtccagtgcaacatccacggtccctctcatcaggctcaccttgctcattgacataacggaatgcgtaccgctctttcagatctgtccatccagagaggggagcaggctccccaccgacgctgtcaaacttgcttcctgcccaaccgaaaacattattgtttgagggggggggggggggggcagattgcatggcgggatatctcgtgaggaacatcactgggacactgtggaacacagtgagtgcagtatgcagagcatgtatgctaggggtcagcgcaggaagggggcctttcccagtctcccatgccactgcaccgtatccacgactcaccaggaccagcttcttgatcggcttccgctcccgtggacaccagtgtgtagcctctggactccaggtatgcgtgcaccgcaaaggccagccgatcgtgccgattcctggggtggaggatatgagtcagccaacttggggctcagagtgcacactggggcacgatacgaaacaacatctacaccgtgtcctccatgctgacacaccacagcttcgctccacctgaatgtgggcgcatgggcccgaatcacagccaatgtcgctgctgccataatgtgatccagaccctctccgcccagatgccgagcggatcgtgggcgctgaatagattcctgtttcgatcactgtttgggtcctttccttttcgtctcggatgcgcgtctcgaaacaggctgcgtcgggctttcggatcccttttgctccctccgtcaccatcctgcgcgcgggcaagttgcttgaccctgggctgtaccagggttggagggtattaccgcgtcaggccattcccagcccggattcaattcaaagtctgggccaccaccctccgccgctctgtctgatcactccacattcgtgcatacactacgttcaagtcctgatccaggcgtgtctcgggacaaggtgtgcttgagtttgaatctcaaggacccactccagcacagctgctggttgaccccgccctcgcaa SEQ ID NO: 23AtTHIC expression cassette comprising Chlorella protothecoides actinpromoter/5′UTR, Arabidopsis thaliana THIC protein coding sequencecodon-optimized for expression in Prototheca moriformis, andChlorella vulgaris nitrate reductase 3′ UTRagtttaggtccagcgtccgtggggggggacgggctgggagcttgggccgggaagggcaagacgatgcagtccctctggggagtcacagccgactgtgtgtgttgcactgtgcggcccgcagcactcacacgcaaaatgcctggccgacaggcaggccctgtccagtgcaacatccacggtccctctcatcaggctcaccttgctcattgacataacggaatgcgtaccgctctttcagatctgtccatccagagaggggagcaggctccccaccgacgctgtcaaacttgcttcctgcccaaccgaaaacattattgtttgagggggggggggggggggcagattgcatggcgggatatctcgtgaggaacatcactgggacactgtggaacacagtgagtgcagtatgcagagcatgtatgctaggggtcagcgcaggaagggggcctttcccagtctcccatgccactgcaccgtatccacgactcaccaggaccagcttcttgatcggcttccgctcccgtggacaccagtgtgtagcctctggactccaggtatgcgtgcaccgcaaaggccagccgatcgtgccgattcctggggtggaggatatgagtcagccaacttggggctcagagtgcacactggggcacgatacgaaacaacatctacaccgtgtcctccatgctgacacaccacagcttcgctccacctgaatgtgggcgcatgggcccgaatcacagccaatgtcgctgctgccataatgtgatccagaccctctccgcccagatgccgagcggatcgtgggcgctgaatagattcctgtttcgatcactgtttgggtcctttccttttcgtctcggatgcgcgtctcgaaacaggctgcgtcgggctttcggatcccttttgctccctccgtcaccatcctgcgcgcgggcaagttgcttgaccctgggctgtaccagggttggagggtattaccgcgtcaggccattcccagcccggattcaattcaaagtctgggccaccaccctccgccgctctgtctgatcactccacattcgtgcatacactacgttcaagtcctgatccaggcgtgtctcgggacaaggtgtgcttgagtttgaatctcaaggacccactccagcacagctgctggttgaccccgccctcgcaatctaga ATGgccgcgtccgtccactgcaccctgatgtccgtggtctgcaacaacaagaaccactccgcccgccccaagctgcccaactcctccctgctgcccggcttcgacgtggtggtccaggccgcggccacccgcttcaagaaggagacgacgaccacccgcgccacgctgacgttcgacccccccacgaccaactccgagcgcgccaagcagcgcaagcacaccatcgacccctcctcccccgacttccagcccatcccctccttcgaggagtgcttccccaagtccacgaaggagcacaaggaggtggtgcacgaggagtccggccacgtcctgaaggtgcccttccgccgcgtgcacctgtccggcggcgagcccgccttcgacaactacgacacgtccggcccccagaacgtcaacgcccacatcggcctggcgaagctgcgcaaggagtggatcgaccgccgcgagaagctgggcacgccccgctacacgcagatgtactacgcgaagcagggcatcatcacggaggagatgctgtactgcgcgacgcgcgagaagctggaccccgagttcgtccgctccgaggtcgcgcggggccgcgccatcatcccctccaacaagaagcacctggagctggagcccatgatcgtgggccgcaagttcctggtgaaggtgaacgcgaacatcggcaactccgccgtggcctcctccatcgaggaggaggtctacaaggtgcagtgggccaccatgtggggcgccgacaccatcatggacctgtccacgggccgccacatccacgagacgcgcgagtggatcctgcgcaactccgcggtccccgtgggcaccgtccccatctaccaggcgctggagaaggtggacggcatcgcggagaacctgaactgggaggtgttccgcgagacgctgatcgagcaggccgagcagggcgtggactacttcacgatccacgcgggcgtgctgctgcgctacatccccctgaccgccaagcgcctgacgggcatcgtgtcccgcggcggctccatccacgcgaagtggtgcctggcctaccacaaggagaacttcgcctacgagcactgggacgacatcctggacatctgcaaccagtacgacgtcgccctgtccatcggcgacggcctgcgccccggctccatctacgacgccaacgacacggcccagttcgccgagctgctgacccagggcgagctgacgcgccgcgcgtgggagaaggacgtgcaggtgatgaacgagggccccggccacgtgcccatgcacaagatccccgagaacatgcagaagcagctggagtggtgcaacgaggcgcccttctacaccctgggccccctgacgaccgacatcgcgcccggctacgaccacatcacctccgccatcggcgcggccaacatcggcgccctgggcaccgccctgctgtgctacgtgacgcccaaggagcacctgggcctgcccaaccgcgacgacgtgaaggcgggcgtcatcgcctacaagatcgccgcccacgcggccgacctggccaagcagcacccccacgcccaggcgtgggacgacgcgctgtccaaggcgcgcttcgagttccgctggatggaccagttcgcgctgtccctggaccccatgacggcgatgtccttccacgacgagacgctgcccgcggacggcgcgaaggtcgcccacttctgctccatgtgcggccccaagttctgctccatgaagatcacggaggacatccgcaagtacgccgaggagaacggctacggctccgccgaggaggccatccgccagggcatggacgccatgtccgaggagttcaacatcgccaagaagacgatctccggcgagcagcacggcgaggtcggcggcgagatctacctgcccgagtcctacgtcaaggccgcgcagaagTGA caattggcagcagcagctcggatagtatcgacacactctggacgctggtcgtgtgatggactgttgccgccacacttgctgccttgacctgtgaatatccctgccgcttttatcaaacagcctcagtgtgtttgatcttgtgtgtacgcgcttttgcgagttgctagctgcttgtgctatttgcgaataccacccccagcatccccttccctcgtttcatatcgcttgcatcccaaccgcaacttatctacgctgtcctgctatccctcagcgctgctcctgctcctgctcactgcccctcgcacagccttggtttgggctccgcctgtattctcctggtactgcaacctgtaaaccagcactgcaatgctgatgcacgggaagtagtgggatgggaacacaaatggaggatccSEQ ID NO: 24PmKASII (Prototheca moriformis KASII) comprising a C. protothecoidesS106 stearoyl-ACP desaturase transit peptideATGgccaccgcatccactttctcggcgttoaatgcccgctgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcgggcgcgccgccgccgccgccgacgccaaccccgcccgccccgagcgccgcgtggtgatcaccggccagggcgtggtgacctccctgggccagaccatcgagcagttctactcctccctgctggagggcgtgtccggcatctcccagatccagaagttcgacaccaccggctacaccaccaccatcgccggcgagatcaagtccctgcagctggacccctacgtgcccaagcgctgggccaagcgcgtggacgacgtgatcaagtacgtgtacatcgccggcaagcaggccctggagtccgccggcctgcccatcgaggccgccggcctggccggcgccggcctggaccccgccctgtgcggcgtgctgatcggcaccgccatggccggcatgacctccttcgccgccggcgtggaggccctgacccgcggcggcgtgcgcaagatgaaccccttctgcatccccttctccatctccaacatgggcggcgccatgctggccatggacatcggcttcatgggccccaactactccatctccaccgcctgcgccaccggcaactactgcatcctgggcgccgccgaccacatccgccgcggcgacgccaacgtgatgctggccggcggcgccgacgccgccatcatcccctccggcatcggcggcttcatcgcctgcaaggccctgtccaagcgcaacgacgagcccgagcgcgcctcccgcccctgggacgccgaccgcgacggcttcgtgatgggcgagggcgccggcgtgctggtgctggaggagctggagcacgccaagcgccgcggcgccaccatcctggccgagctggtgggcggcgccgccacctccgacgcccaccacatgaccgagcccgacccccagggccgcggcgtgcgcctgtgcctggagcgcgccctggagcgcgcccgcctggcccccgagcgcgtgggctacgtgaacgcccacggcacctccacccccgccggcgacgtggccgagtaccgcgccatccgcgccgtgatcccccaggactccctgcgcatcaactccaccaagtccatgatcggccacctgctgggcggcgccggcgccgtggaggccgtggccgccatccaggccctgcgcaccggctggctgcaccccaacctgaacctggagaaccccgcccccggcgtggaccccgtggtgctggtgggcccccgcaaggagcgcgccgaggacctggacgtggtgctgtccaactccttcggcttcggcggccacaactcctgcgtgatcttccgcaagtacgacgagatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagTGA SEQ ID NO: 25PmKASII (Prototheca moriformis KASII) comprising a C. protothecoidesS106 stearoylACP desaturase transit peptideMATASTESAFNARCGDLRRSAGSGPRRPARPLPVRGRAAAAADANPARPERRVVITGQGVVISLGQIIEQFYSSLLEGVSGISQIQKFDTTGYTTTIAGEIKSLQLDPYVPKRWAKRVDDVIKYVYIAGKQALESAGLPIEAAGLAGAGLDPALCGVLIGTAMAGMTSFAAGVEALTRGGVRKMNPFCIPFSISNMGGAMLAMDIGFMGPNYSISTACATGNYCILGAADHIRRGDANVMLAGGADAAIIPSGIGGFIACKALSKRNDEPERASRPWDADRDGFVMGEGAGVLVLEELEHAKRRGATILAELVGGAATSDAHHMTEPDPQGRGVRLCLERALERARLAPERVGYVNAHGTSTPAGDVAEYRAIRAVIPQDSLRINSTKSMIGHLLGGAGAVEAVAAIQALRTGWLHPNLNLENPAPGVDPVVLVGPRKERAEDLDVVLSNSFGFGGHNSCVIFRKYDEMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 26Codon-optimized Prototheca moriformis (UTEX 1435) FAD2 protein-coding sequenceATGgccatcaagaccaaccgccagcccgtggagaagccccccttcaccatcggcaccctgcgcaaggccatccccgcccactgcttcgagcgctccgccctgcgctcctccatgtacctggccttcgacatcgccgtgatgtccctgctgtacgtggcctccacctacatcgaccccgcccccgtgcccacctgggtgaagtacggcgtgatgtggcccctgtactggttcttccagggcgccttcggcaccggcgtgtgggtgtgcgcccacgagtgcggccaccaggccttctcctcctcccaggccatcaacgacggcgtgggcctggtgttccactccctgctgctggtgccctactactcctggaagcactcccaccgccgccaccactccaacaccggctgcctggacaaggacgaggtgttcgtgcccccccaccgcgccgtggcccacgagggcctggagtgggaggagtggctgcccatccgcatgggcaaggtgctggtgaccctgaccctgggctggcccctgtacctgatgttcaacgtggcctcccgcccctacccccgcttcgccaaccacttcgacccctggtcccccatcttctccaagcgcgagcgcatcgaggtggtgatctccgacctggccctggtggccgtgctgtccggcctgtccgtgctgggccgcaccatgggctgggcctggctggtgaagacctacgtggtgccctacctgatcgtgaacatgtggctggtgctgatcaccctgctgcagcacacccaccccgccctgccccactacttcgagaaggactgggactggctgcgcggcgccatggccaccgtggaccgctccatgggcccccccttcatggacaacatcctgcaccacatctccgacacccacgtgctgcaccacctgttctccaccatcccccactaccacgccgaggaggcctccgccgccatccgccccatcctgggcaagtactaccagtccgactcccgctgggtgggccgcgccctgtgggaggactggcgcgactgccgctacgtggtgcccgacgcccccgaggacgactccgccctgtggttccacaagTAG SEQ ID NO: 27Amino acid sequence of Prototheca moriformis FAD2MAIKTNRQPVEKPPFTIGILRKAIPAHCFERSALRSSMYLAFDIAVMSLLYVASTYIDPAPVPIWVKYGVMWPLYWFFQGAFGTGVWVCAHECGHQAFSSSQAINDGVGLVFHSLLLVPYYSWKHSHRRHHSNTGCLDKDEVFVPPHRAVAHEGLEWEEWLPIRMGKVLVTLTLGWPLYLMFNVASRPYPRFANHFDPWSPIFSKRERIEVVISDLALVAVLSGLSVLGRTMGWAWLVKTYVVPYLIVNMWLVLITLLQHTHPALPHYFEKDWDWLRGAMATVDRSMGPPFMDNILHHISDTHVLHHLFSTIPHYHAEEASAAIRPILGKYYQSDSRWVGRALWEDWRDCRYVVPDAPEDDSALWFHK SEQ ID NO: 28Codon-optimized coding region of Brassica napus C18:0-preferringthioesterase from pSZ1358ACTAGTATGCTGAAGCTGTCCTGCAACGTGACCAACAACCTGCACACCTTCTCCTTCTTCTCCGACTCCTCCCTGTTCATCCCCGTGAACCGCCGCACCATCGCCGTGTCCTCCGGGCGCGCCTCCCAGCTGCGCAAGCCCGCCCTGGACCCCCTGCGCGCCGTGATCTCCGCCGACCAGGGCTCCATCTCCCCCGTGAACTCCTGCACCCCCGCCGACCGCCTGCGCGCCGGCCGCCTGATGGAGGACGGCTACTCCTACAAGGAGAAGTTCATCGTGCGCTCCTACGAGGTGGGCATCAACAAGACCGCCACCGTGGAGACCATCGCCAACCTGCTGCAGGAGGTGGCCTGCAACCACGTGCAGAAGTGCGGCTTCTCCACCGACGGCTTCGCCACCACCCTGACCATGCGCAAGCTGCACCTGATCTGGGTGACCGCCCGCATGCACATCGAGATCTACAAGTACCCCGCCTGGTCCGACGTGGTGGAGATCGAGACCTGGTGCCAGTCCGAGGGCCGCATCGGCACCCGCCGCGACTGGATCCTGCGCGACTCCGCCACCAACGAGGTGATCGGCCGCGCCACCTCCAAGTGGGTGATGATGAACCAGGACACCCGCCGCCTGCAGCGCGTGACCGACGAGGTGCGCGACGAGTACCTGGTGTTCTGCCCCCGCGAGCCCCGCCTGGCCTTCCCCGAGGAGAACAACTCCTCCCTGAAGAAGATCCCCAAGCTGGAGGACCCCGCCCAGTACTCCATGCTGGAGCTGAAGCCCCGCCGCGCCGACCTGGACATGAACCAGCACGTGAACAACGTGACCTACATCGGCTGGGTGCTGGAGTCCATCCCCCAGGAGATCATCGACACCCACGAGCTGCAGGTGATCACCCTGGACTACCGCCGCGAGTGCCAGCAGGACGACATCGTGGACTCCCTGACCACCTCCGAGATCCCCGACGACCCCATCTCCAAGTTCACCGGCACCAACGGCTCCGCCATGTCCTCCATCCAGGGCCACAACGAGTCCCAGTTCCTGCACATGCTGCGCCTGTCCGAGAACGGCCAGGAGATCAACCGCGGCCGCACCCAGTGGCGCAAGAAGTCCTCCCGCATGGACTACAAGGACCACGACGGCGACTACAAGGACCACGACATCGACTACAAGGACGACGACGACAAGTGAATCGAT SEQ ID NO: 29Amino acid sequence of Brassica napus C18:0-preferring thioesterase(Accession No. CAA52070.1)MLKLSCNVTNNLHTFSFFSDSSLFIPVNRRTIAVSSSQLRKPALDPLRAVISADQGSISPVNSCTPADRLRAGRLMEDGYSYKEKFIVRSYEVGINKTATVETIANLLQEVACNHVQKCGESIDGFATTLIMRKLHLIWVTARMHIETYKYPAWSDVVEIETWCQSEGRIGIRRDWILRDSATNEVIGRATSKWVMMNQDTRRLQRVTDEVRDEYLVFCPREPRLAFPEENNSSLKKIPKLEDPAQYSMLELKPRRADLDMNQHVNNVTYIGWVLESIPQEIIDTHELQVITLDYRRECQQDDIVDSLTTSEIPDDPISKFTGTNGSAMSSIQGHNESQFLHMLRLSENGQEINRGRTQWRKKSSR SEQ ID NO: 30Prototheca moriformis FATA1 allele 1 5′ homology donor regionGGAGTCACTGTGCCACTGAGTTCGACTGGTAGCTGAATGGAGTCGCTGCTCCACTAAACGAATTGTCAGCACCGCCAGCCGGCCGAGGACCCGAGTCATAGCGAGGGTAGTAGCGCGCCATGGCACCGACCAGCCTGCTTGCCAGTACTGGCGTCTCTTCCGCTTCTCTGTGGTCCTCTGCGCGCTCCAGCGCGTGCGCTTTTCCGGTGGATCATGCGGICCGTGGCGCACCGCAGCGGCCGCTGCCCATGCAGCGCCGCTGCTTCCGAACAGTGGCGGTCAGGGCCGCACCCGCGGTAGCCGTCCGTCCGGAACCCGCCCAAGAGTTTTGGGAGCAGCTTGAGCCCTGCAAGATGGCGGAGGACAAGCGCATCTTCCTGGAGGAGCACCGGTGCGTGGAGGTCCGGGGCTGACCGGCCGTCGCATTCAACGTAATCAATCGCATGATGATCAGAGGACACGAAGTCTTGGTGGCGGTGGCCAGAAACACTGTCCATTGCAAGGGCATAGGGATGCGTTCCTTCACCTCTCATTTCTCATTTCTGAATCCCTCCCTGCTCACTCTTTCTCCTCCTCCTTCCCGTTCACGCAGCATTCGG SEQ ID NO: 31Prototheca moriformis FATA1 allele 1 3′ homology donor regionGACAGGGTGGTTGGCTGGATGGGGAAACGCTGGTCGCGGGATTCGATCCTGCTGCTTATATCCTCCCTGGAAGCACACCCACGACTCTGAAGAAGAAAACGTGCACACACACAACCCAACCGGCCGAATATTTGCTTCCTTATCCCGGGTCCAAGAGAGACTGCGATGCCCCCCTCAATCAGCATCCTCCTCCCTGCCGCTTCAATCTTCCCTGCTTGCCTGCGCCCGCGGTGCGCCGTCTGCCCGCCCAGTCAGTCACTCCTGCACAGGCCCCTTGTGCGCAGTGCTCCTGTACCCTTTACCGCTCCTTCCATTCTGCGAGGCCCCCTATTGAATGTATTCGTTGCCTGTGTGGCCAAGCGGGCTGCTGGGCGCGCCGCCGTCGGGCAGTGCTCGGCGACTTTGGCGGAAGCCGATTGTTCTTCTGTAAGCCACGCGCTTGCTGCTTTGGGAAGAGAAGGGGGGGGGTACTGAATGGATGAGGAGGAGAAGGAGGGGTATTGGTATTATCTGAGTTGGGT SEQ ID NO: 32Prototheca moriformis FATA1 allele 2 5′ homology donor regionAATGGAGTCGCTGCTCCACTAATCGAATTGTCAGCACCGCCAGCCGGCCGAGGACCCGAGTCATAGCGAGGGTAGTAGCGCGCCATGGCACCGACCAGCCTGCTTGCCCGTACTGGCGTCTCTTCCGCTTCTCTGTGCTCCTCTACGCGCTCCGGCGCGTGCGCTTTTCCGGTGGATCATGCGGTCCGTGGCGCACCGCAGCGGCCGCTGCCCATGCAGCGCCGCTGCTTCCGAACAGTGGCTGTCAGGGCCGCACCCGCAGTAGCCGTCCGTCCGGAACCCGCCCAAGAGTTTTGGGAGCAGCTTGAGCCCTGCAAGATGGCGGAGGACAAGCGCATCTTCCTGGAGGAGCACCGGTGCGCGGAGGTCCGGGGCTGACCGGCCGTCGCATTCAACGTAATCAATCGCATGATGATCACAGGACGCGACGTCTTGGTGGCGGTGGCCAGGGACACTGCCCATTGCACAGGCATAGGAATGCGTTCCTTCTCATTTCTCAGTTTTCTGAGCCCCTCCCTCTTCACTCTTTCTCCTCCTCCTCCCCTCTCACGCAGCATTCGTGG SEQ ID NO: 33Prototheca moriformis FATA1 allele 2 3′ homology donor regionCACTAGTATCGATTTCGAACAGAGGAGAGGGTGGCTGGTAGTTGCGGGATGGCTGGTCGCCCGTCGATCCTGCTGCTGCTATTGTCTCCTCCTGCACAAGCCCACCCACGACTCCGAAGAAGAAGAAGAAAACGCGCACACACACAACCCAACCGGCCGAATATTTGCTTCCTTATCCCGGGTCCAAGAGAGACGGCGATGCCCCCCTCAATCAGCCTCCTCCTCCCTGCCGCTCCAATCTTCCCTGCTTGCATGCGCCCGCGAGAGGCTGTCTGCGCGCCCCGTCAGTCACTCCCCGTGCAGACGCCTCGTGCTCGGTGCTCCTGTATCCTTTACCGCTCCTTTCATTCTGCGAGGCCCCCTGTTGAATGTATTCGTTGCCTGTGTGGCCAAGCGCGCTGCTGGGCGCGCCGCCGTCGGGCGGTGCTCGGCGACTCTGGCGGAAGCCGGTTGTTCTTCTGTAAGCCACGCGCTTGCTGCTTTTGGAAAAGAGGGGGGTTTACTGAATGGAGGAGGAGCAGGATAATTGGTAGTATCTGAGTTG TTGSEQ ID NO: 34 SAD2 hairpin CactagtGCGCTGGACGCGGCAGTGGGTGGCCGAGGAGAACCGGCACGGCGACCTGCTGAACAAGTACTGTTGGCTGACGGGGCGCGTCAACATGCGGGCCGTGGAGGTGACCATCAACAACCTGATCAAGAGCGGCATGAACCCGCAGACGGACAACAACCCTTACTTGGGCTTCGTCTACACCTCCTTCCAGGAGCGCGCGACCAAGTACAGCCACGGCAACACCGCGCGCCTTGCGGCCGAGCAGTGTGTTTGAGGGTTTTGGTTGCCCGTATCGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccTGCTCGGCCGCAAGGCGCGCGGTGTTGCCGTGGCTGTACTTGGTCGCGCGCTCCTGGAAGGAGGTGTAGACGAAGCCCAAGTAAGGGTTGTTGTCCGTCTGCGGGTTCATGCCGCTCTTGATCAGGTTGTTGATGGTCACCTCCACGGCCCGCATGTTGACGCGCCCCGTCAGCCAACAGTACTTGTTCAGCAGGTCGCCGTGCCGGTTCTCCTCGGCCACCCACTGCCGCGTCCAGCGCaag cttSEQ ID NO: 35 Prototheca moriformis FAD-D omega 3 desaturaseMSIQFALRAAYIKGICQRLSGRGAALGLSRDWIPGWILPRCWPASAAATAPPRARHQERAIHLTSGRRRHSALASDADERALPSNAPGLVMASQANYFRVRLLPEQEEGELESWSPNVRHTTLLCKPRAMLSKLQMRVMVGDRVIVTAIDPVNMTVHAPPFDPLPATRFLVAGEAADMDITVVLNKADLVPEEESAALAQEVASWGPVVLTSTLTGRGLQELERQLGSTTAVLAGPSGAGKSSIINALARAARERPSDASVSNVPEEQVVGEDGRALANPPPFTLADIRNAIPKDCFRKSAAKSLAYLGDLSITGMAVLAYKINSPWLMPLYWFAQGTMFWALFVVGHDCGHQSFSTSKRLNDALAWLGALAAGTWTWALGVLPMLNLYLAPYVWLLVTYLHHHGPSDPREEMPWYRGREWSYMRGGLTTIDRDYGLFNKVHHDIGTHVVHH SEQ ID NO: 36MFWALFVVGHDCGHQSFSTSKRLNDAVGLFVHSTIGVPYHGWRISHRTHHNNHGHVENDESWYPPTESGLKAMTDMGRQGRFHFPSMLFVYPFYLFWRSPGKTGSHFSPATDLFALWEAPLIRTSNACQLAWLGALAAGTWALGVLPMLNLYLAPYVISVAWLDLVTYLHHHGPSDPREEMPWYRGREWSYMRGGLTTIDRDYGLFNKVHHDIGTHVVHHLFPQIPHYNLCRATKAAKKVLGPYYREPERCPLGLLPVHLLAPLLRSLGQDHFVDDAGSVLFYRRAEGINPWIQKLLPWLGGARRGADAQRDAAQ SEQ ID NO: 37Camelina sativa omega-3 EAD7-2MANLVLSECGIRPLPRIYTTPRSNFVSNNNKPIFKFRPFTSYKTSSSPLACSRDGFGKNWSLNVSVPLTTTTPIVDESPLKEEEEEKQRFDPGAPPPFNLADIRAAIPKHCWVKNPWKSMSYVLRDVAIVFALAAGASYLNNWIVWPLYWLAQGTMFWALFVLGHDCGHGSFSNNPRLNNVVGHLLHSSILVPYHGWRISHRTHHQNHGHVENDESWHPMSEKIYQSLDKPTRFFRFTLPLVMLAYPFYLWARSPGKKGSHYHPESDLFLPKEKTDVLTSTACWTAMAALLICLNFVVGPVQMLKLYGIPYWINVMWLDFVTYLHHHGHEDKLPWYRGKEWSYLRGGLTTLDRDYGVINNIHHDIGTHVIHHLFPQIPHYHLVEATEAVKPVLGKYYREPDKSGPLPLHLLGILAKSIKEDHYVSDEGDVVYYKADPNMYGEIKVGAD SEQ ID NO: 38Prototheca moriformis delta 12 desaturase allele 2MAIKTNRQPVEKPPFTIGILRKAIPAHCFERSALRSSMYLAFDIAVMSLLYVASTYIDPAPVPIWVKYGIMWPLYWFFQGAFGTGVWVCAHECGHQAFSSSQAINDGVGLVFHSLLLVPYYSWKHSHRRHHSNTGCLDKDEVFVPPHRAVAHEGLEWEEWLPIRMGKVLVTLTLGWPLYLMFNVASRPYPRFANHFDPWSPIFSKRERIEVVISDLALVAVLSGLSVLGRTMGWAWLVKTYVVPYMIVNMWLVLITLLQHTHPALPHYFEKDWDWLRGAMATVDRSMGPPFMDSILHHISDTHVLHHLFSTIPHYHAEEASAAIRPILGKYYQSDSRWVGRALWEDWRDCRYVVPDAPEDDSALWFHK SEQ ID NO: 39Camelina sativa omega-3 FAD7-1MANLVLSECGIRPLPRIYTTPRSNFVSNNNKPIFKFRPLTSYKTSSPLFCSRDGFGRNWSLNVSVPLATTTPIVDESPLEEEEEEEKQRFDPGAPPPFNLADIRAAIPKHCWVKNPWKSMSYVLRDVAIVFALAAGAAYLNNWIVWPLYWLAQGTMFWALFVLGHDCGHGSFSNNPRLNNVVGHLLHSSILVPYHGWRISHRTHHQNHGHVENDESWHPMSEKIYQSLDKPTRFFRFTLPLVMLAYPFYLWARSPGKKGSHYHPESDLFLPKEKTDVLTSTACWTAMAALLICLNFVVGPVQMLKLYGIPYWINVMWLDFVTYLHHHGHEDKLPWYRGKEWSYLRGGLTTLDRDYGVINNIHHDIGTHVIHHLFPQIPHYHLVEATEAVKPVLGKYYREPDKSGPLPLHLLGILAKSIKEDHYVSDEGDVVYYKADPNMYGEIKVGAD SEQ ID NO: 40 PmFATA-hpBactagtCATTCGGGGCAACGAGGTGGGCCCCICGCAGCGGCTGACGATCACGGCGGTGGCCAACATCCTGCAGGAGGCGGCGGGCAACCACGCGGTGGCCATGTGGGGCCGGAGCGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccGCTCCGGCCCCACATGGCCACCGCGTGGTTGCCCGCCGCCTCCTGCAGGATGTTGGCCACCGCCGTGATCGTCAGCCGCTGCGAGGGGCCCACCTCGTTGCCCCGAATGaagctt SEQ ID NO: 41 PmFATA-hpCactagtGGAGGGTTTCGCGACGGACCCGGAGCTGCAGGAGGCGGGTCTCATCTTTGTGATGACGCGCATGCAGATCCAGATGTACCGCTACCCGCGCTGGGGCGACCTGATGCAGGTGGAGACCTGGTTCCAGAGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccTCTGGAACCAGGTCTCCACCTGCATCAGGTCGCCCCAGCGCGGGTAGCGGTACATCTGGATCTGCATGCGCGTCATCACAAAGATGAGACCCGCCTCCTGCAGCTCCGGGTCCGTCGCGAAACCCTCCaagctt SEQ ID NO: 42PmFATA-hpDactagtCGGCGGGCAAGCTGGGCGCGCAGCGCGAGTGGGTGCTGCGCGACAAGCTGACCGGCGAGGCGCTGGGCGCGGCCACCTCGAGCTGGGTCATGATCAACATCCGCACGCGCCGGCCGTGCCGCATGCCGGGTGTGTTTGAGGGTTTTGGTTGCCCGTATCGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccCCGGCATGCGGCACGGCCGGCGCGTGCGGATGTTGATCATGACCCAGCTCGAGGTGGCCGCGCCCAGCGCCTCGCCGGTCAGCTTGTCGCGCAGCACCCACTCGCGCTGCGCGCCCAGCTTGCCCGCCGaagctt SEQ ID NO: 43PmFATA-hpEactagtGTCCGCGTCAAGTCGGCCTTCTTCGCGCGCGAGCCGCCGCGCCTGGCGCTGCCGCCCGCGGTCACGCGTGCCAAGCTGCCCAACATCGCGACGCCGGCGCCGCTGCGCGGGCACCGCCAGGTCGCGCGCCGCACCGACATGGACATGAACGGGCACGTGAACAACGTGGCCTACCTGGCCTGGTGCCTGGAGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccTCCAGGCACCAGGCCAGGTAGGCCACGTTGTTCACGTGCCCGTTCATGTCCATGTCGGTGCGGCGCGCGACCTGGCGGTGCCCGCGCAGCGGCGCCGGCGTCGCGATGTTGGGCAGCTTGGCACGCGTGACCGCGGGCGGCAGCGCCAGGCGCGGCGGCTCGCGCGCGAAGAAGGCCGACTTGACGCGGACaagott SEQ ID NO: 44 PmFATA-hpFactagtCCGTGCCCGAGCACGTCTTCAGCGACTACCACCTCTACCAGATGGAGATCGACTTCAAGGCCGAGTGCCACGCGGGCGACGTCATCTCCTCCCAGGCCGAGCAGATCCCGCCCCAGGAGGCGCTCACGCACAACGGCGCCGGCCGCAACCCCTCCTGCTTCGTCCATAGCATTCTGCGCGCCGAGACCGAGCGTGTGTTTGAGGGTTTTGGTTGCCCGTATCGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccGCTCGGTCTCGGCGCGCAGAATGCTATGGACGAAGCAGGAGGGGTTGCGGCCGGCGCCGTTGTGCGTGAGCGCCTCCTGGGGCGGGATCTGCTCGGCCTGGGAGGAGATGACGTCGCCCGCGTGGCACTCGGCCTTGAAGTCGATCTCCATCTGGTAGAGGTGGTAGTCGCTGAAGACGTGCTCGGGCACGGaagctt SEQ ID NO: 45 PmFATA-hpGactagtTCGTCCGCGCGCGAACCACATGGTCGGCCCCCATCGACGCGCCCGCCGCCAAGCCGCCCAAGGCGAGCCACTGAGGACAGGGTGGTTGGCTGGATGGGGAAACGCTGGTCGCGGGATTCGATCCTGCTGCTTATATCCTCGTGTGTTTGAGGGTTTTGGTTGCCCGTATTGAGGTCCTGGTGGCGCGCATGGGGGAGAAGGCGCCTGTCCCGCTGACCCCCCCGGCTACCCTCCCGGCACCTTCCAGGGCGCGTACGggatccGAGGATATAAGCAGCAGGATCGAATCCCGCGACCAGCGTTTCCCCATCCAGCCAACCACCCTGTCCTCAGTGGCTCGCCTTGGGCGGCTTGGCGGCGGGCGCGTCGATGGGGGCCGACCATGTGGTTCGCGCGCGGACGAaagctt SEQ ID NO: 46 Codon-optimized Cuphea wrightii KASAIATGGCCGCCGCCGCCAGCATGGTGGCCAGCCCCTTCTGCACCTGGCTGGTGGCCAGCTGCATGAGCACCAGCTTCGACAACGACCCCCGCAGCCCCAGCGTGAAGCGCTTCCCCCGCCGCAAGCGCGTGCTGAGCCAGCGCGGCAGCACCTACGTATTCCAGTGCCTGGTGGCCAGCTGCATCGACCCCTGCGACCAGTACCGCAGCAGCGCCAGCCTGAGCTTCCTGGGCGACAACGGCTTCGCCAGCCTGTTCGGCAGCAAGCCCTTCATGAGCAACCGCGGCCACCGCCGCCTGCGCCGCGCCAGCCACAGCGGCGAGGCCATGGCCGIGGCCCTGCAGCCCGCCCAGGAGGCCGGCACCAAGAAGAAGCCCGTGATCAAGCAGCGCCGCGTGGTGGTGACCGGCATGGGCGTGGTGACCCCCCTGGGCCACGAGCCCGACGTGTTCTACAACAACCTGCTGGACGGCGTGAGCGGCATCAGCGAGATCGAGACCTTCGACTGCACCCAGTTCCCCACCCGCATCGCCGGCGAGATCAAGAGCTTCAGCACCGACGGCTGGGTGGCCCCCAAGCTGAGCAAGCGCATGGACAAGTTCATGCTGTACCTGCTGACCGCCGGCAAGAAGGCCCTGGCCGACGGCGGCATCACCGACGAGGTGATGAAGGAGCTGGACAAGCGCAAGTGCGGCGTGCTGATCGGCAGCGGCATGGGCGGCATGAAGGTGTTCAACGACGCCATCGAGGCCCTGCGCGTGAGCTACAAGAAGATGAACCCCTTCTGCGTGCCCTTCGCCACCACCAACATGGGCAGCGCCATGCTGGCCATGGACCTGGGCTGGATGGGCCCCAACTACAGCATCAGCACCGCCTGCGCCACCAGCAACTTCTGCATCCTGAACGCCGCCAACCACATCATCCGCGGCGAGGCCGACATGATGCTGTGCGGCGGCAGCGACGCCGTGATCATCCCCATCGGCCTGGGCGGCTTCGTGGCCTGCCGCGCCCTGAGCCAGCGCAACAGCGACCCCACCAAGGCCAGCCGCCCCTGGGACAGCAACCGCGACGGCTTCGTGATGGGCGAGGGCGCCGGCGTGCTGCTGCTGGAGGAGCTGGAGCACGCCAAGAAGCGCGGCGCCACCATCTACGCCGAGTTCCTGGGCGGCAGCTTCACCTGCGACGCCTACCACATGACCGAGCCCCACCCCGAGGGCGCCGGCGTGATCCTGTGCATCGAGAAGGCCCTGGCCCAGGCCGGCGTGAGCAAGGAGGACGTGAACTACATCAACGCCCACGCCACCAGCACCAGCGCCGGCGACATCAAGGAGTACCAGGCCCTGGCCCGCTGCTTCGGCCAGAACAGCGAGCTGCGCGTGAACAGCACCAAGAGCATGATCGGCCACCTGCTGGGCGCCGCCGGCGGCGTGGAGGCCGTGACCGTGGTGCAGGCCATCCGCACCGGCTGGATTCACCCCAACCTGAACCTGGAGGACCCCGACAAGGCCGTGGACGCCAAGCTGCTGGTGGGCCCCAAGAAGGAGCGCCTGAACGTGAAGGTGGGCCTGAGCAACAGCTTCGGCTTCGGCGGCCACAACAGCAGCATCCTGTTCGCCCCCTGCAACGTGTGASEQ ID NO: 47Codon-optimized Cuphea wrightii KASAI with P. moriformis SAD transitpeptideATGGGCCGCGGTGTCTCCCTTCCCCGGCCCAGGGTCGCGGTGCGCGCCCAGTCGGCGAGTCAGGTTTTGGAGAGCTGTATTCCAGTGCCTGGTGGCCAGCTGCATCGACCCCTGCGACCAGTACCGCAGCAGCGCCAGCCTGAGCTTCCTGGGCGACAACGGCTTCGCCAGCCTGTTCGGCAGCAAGCCCTTCATGAGCAACCGCGGCCACCGCCGCCTGCGCCGCGCCAGCCACAGCGGCGAGGCCATGGCCGTGGCCCTGCAGCCCGCCCAGGAGGCCGGCACCAAGAAGAAGCCCGTGATCAAGCAGCGCCGCGTGGTGGTGACCGGCATGGGCGTGGTGACCCCCCTGGGCCACGAGCCCGACGTGTTCTACAACAACCTGCTGGACGGCGTGAGCGGCATCAGCGAGATCGAGACCTTCGACTGCACCCAGTTCCCCACCCGCATCGCCGGCGAGATCAAGAGCTTCAGCACCGACGGCTGGGTGGCCCCCAAGCTGAGCAAGCGCATGGACAAGTTCATGCTGTACCTGCTGACCGCCGGCAAGAAGGCCCTGGCCGACGGCGGCATCACCGACGAGGTGATGAAGGAGCTGGACAAGCGCAAGTGCGGCGTGCTGATCGGCAGCGGCATGGGCGGCATGAAGGTGTTCAACGACGCCATCGAGGCCCTGCGCGTGAGCTACAAGAAGATGAACCCCTTCTGCGTGCCCTTCGCCACCACCAACATGGGCAGCGCCATGCTGGCCATGGACCTGGGCTGGATGGGCCCCAACTACAGCATCAGCACCGCCTGCGCCACCAGCAACTTCTGCATCCTGAACGCCGCCAACCACATCATCCGCGGCGAGGCCGACATGATGCTGTGCGGCGGCAGCGACGCCGTGATCATCCCCATCGGCCTGGGCGGCTTCGTGGCCTGCCGCGCCCTGAGCCAGCGCAACAGCGACCCCACCAAGGCCAGCCGCCCCTGGGACAGCAACCGCGACGGCTTCGTGATGGGCGAGGGCGCCGGCGTGCTGCTGCTGGAGGAGCTGGAGCACGCCAAGAAGCGCGGCGCCACCATCTACGCCGAGTTCCTGGGCGGCAGCTTCACCTGCGACGCCTACCACATGACCGAGCCCCACCCCGAGGGCGCCGGCGTGATCCTGTGCATCGAGAAGGCCCTGGCCCAGGCCGGCGTGAGCAAGGAGGACGTGAACTACATCAACGCCCACGCCACCAGCACCAGCGCCGGCGACATCAAGGAGTACCAGGCCCTGGCCCGCTGCTTCGGCCAGAACAGCGAGCTGCGCGTGAACAGCACCAAGAGCATGATCGGCCACCTGCTGGGCGCCGCCGGCGGCGTGGAGGCCGTGACCGTGGTGCAGGCCATCCGCACCGGCTGGATTCACCCCAACCTGAACCTGGAGGACCCCGACAAGGCCGTGGACGCCAAGCTGCTGGTGGGCCCCAAGAAGGAGCGCCTGAACGTGAAGGTGGGCCTGAGCAACAGCTTCGGCTTCGGCGGCCACAACAGCAGCATCCTGTTCGCCCCCTGCAACGTGTGA SEQ ID NO: 48Codon-optimized Cuphea pulcherrima KASIVATGCCCGCGGCCAGCTCGCTGCTGGCGTCCCCCCTGTGCACCTGGCTGCTGGCCGCGTGCATGAGCACCTCGTTCCACCCCTCCGACCCCCTGCCCCCCAGCATCTCGTCCCCCCGCCGCCGCCTGAGCCGCCGCCGCATCCTGTCGCAGTGCGCCCCCCTGCCCTCCGCGAGCTCGGCCCTGCGCGGCTCCAGCTTCCACACCCTGGTGACCTCGTATCTGGCGTGCTTCGAGCCCTGCCACGACTATTATACCAGCGCCTCCCTGTTCGGCTCGCGCCCCATCCGCACCACCCGCCGCCACCGCCGCCTGAACCGCGCGAGCCCCICGCGCGAGGCGATGGCGGTCGCCCTGCAGCCCGAGCAGGAGGTGACCACCAAGAAGAAGCCCTCCATCAAGCAGCGCCGCGTCGTGGTCACCGGCATGGGCGTGGTCACCCCCCTGGGCCACGACCCCGACGTGTTCTATAACAACCTGCTGGACGGCACCAGCGGCATCTCGGAGATCGAGACCTTCGACTGCGCGCAGTTCCCCACCCGCATCGCCGGCGAGATCAAGTCCTTCAGCACCGACGGCTGGGTCGCGCCCAAGCTGTCGAAGCGCATGGACAAGTTCATGCTGTATATGCTGACCGCCGGCAAGAAGGCGCTGACCGACGGCGGCATCACCGAGGACGTGATGAAGGAGCTGGACAAGCGCAAGTGCGGCGTCCTGATCGGCTCCGCGATGGGCGGCATGAAGGTGTTCAACGACGCGATCGAGGCCCTGCGCATCAGCTATAAGAAGATGAACCCCTTCTGCGTGCCCTTCGCGACCACCAACATGGGCTCGGCCATGCTGGCGATGGACCTGGGCTGGATGGGCCCCAACTATTCCATCAGCACCGCCTGCGCGACCTCGAACTTCTGCATCATGAACGCGGCCAACCACATCATCCGCGGCGAGGCGGACGTCATGCTGTGCGGCGGCTCCGACGCCGTGATCATCCCCATCGGCATGGGCGGCTTCGTCGCGTGCCGCGCCCTGAGCCAGCGCAACTCGGACCCCACCAAGGCGTCCCGCCCCTGGGACAGCAACCGCGACGGCTTCGTGATGGGCGAGGGCGCCGGCGTCCTGCTGCTGGAGGAGCTGGAGCACGCGAAGAAGCGCGGCGCCACCATCTATGCGGAGTTCCTGGGCGGCTCGTTCACCTGCGACGCCTATCACATGACCGAGCCCCACCCCGACGGCGCCGGCGTGATCCTGTGCATCGAGAAGGCGCTGGCCCAGTCCGGCGTCAGCCGCGAGGACGTGAACTATATCAACGCGCACGCCACCTCGACCCCCGCGGGCGACATCAAGGAGTATCAGGCCCTGATCCACTGCTTCGGCCAGAACCGCGAGCTGAAGGTCAACTCCACCAAGAGCATGATCGGCCACCTGCTGGGCGCGGCGGGCGGCGTGGAGGCGGTCTCGGTGGTCCAGGCCATCCGCACCGGCTGGATCCACCCCAACATCAACCTGGAGAACCCCGACGAGGGCGTGGACACCAAGCTGCTGGTGGGCCCCAAGAAGGAGCGCCTGAACGTCAAGGTGGGCCTGTCCAACAGCTTCGGCTTCGGCGGCCACAACTCGTCCATCCTGTTCGCGCCCTATATCTGA SEQ ID NO: 49 Codon-optimized Cuphea hookeriana KASIVATGGTGGCCGCCGCCGCCTCCAGCGCCTTCTTCCCCGTGCCCGCCCCCGGCGCCTCCCCCAAGCCCGGCAAGTTCGGCAACTGGCCCTCCAGCCTGAGCCCCTCCTTCAAGCCCAAGTCCATCCCCAACGGCGGCTTCCAGGTGAAGGCCAACGACAGCGCCCACCCCAAGGCCAACGGCTCCGCCGTGAGCCTGAAGAGCGGCAGCCTGAACACCCAGGAGGACACCTCCTCCAGCCCCCCCCCCCGCACCTTCCTGCACCAGCTGCCCGACTGGAGCCGCCTGCTGACCGCCATCACCACCGTGTTCGTGAAGTCCAAGCGCCCCGACATGCACGACCGCAAGTCCAAGCGCCCCGACATGCTGGTGGACAGCTTCGGCCTGGAGTCCACCGTGCAGGACGGCCTGGTGTTCCGCCAGTCCTTCTCCATCCGCTCCTACGAGATCGGCACCGACCGCACCGCCAGCATCGAGACCCTGATGAACCACCTGCAGGAGACCTCCCTGAACCACTGCAAGAGCACCGGCATCCTGCTGGACGGCTTCGGCCGCACCCTGGAGATGTGCAAGCGCGACCTGATCTGGGTGGTGATCAAGATGCAGATCAAGGTGAACCGCTACCCCGCCTGGGGCGACACCGTGGAGATCAACACCCGCTTCAGCCGCCTGGGCAAGATCGGCATGGGCCGCGACTGGCTGATCTCCGACTGCAACACCGGCGAGATCCTGGTGCGCGCCACCAGCGCCTACGCCATGATGAACCAGAAGACCCGCCGCCTGTCCAAGCTGCCCTACGAGGTGCACCAGGAGATCGTGCCCCTGTTCGTGGACAGCCCCGTGATCGAGGACTCCGACCTGAAGGTGCACAAGTTCAAGGTGAAGACCGGCGACAGCATCCAGAAGGGCCTGACCCCCGGCTGGAACGACCTGGACGTGAACCAGCACGTGTCCAACGTGAAGTACATCGGCTGGATCCTGGAGAGCATGCCCACCGAGGTGCTGGAGACCCAGGAGCTGTGCTCCCTGGCCCTGGAGTACCGCCGCGAGTGCGGCCGCGACTCCGTGCTGGAGAGCGTGACCGCCATGGACCCCAGCAAGGTGGGCGTGCGCTCCCAGTACCAGCACCTGCTGCGCCTGGAGGACGGCACCGCCATCGTGAACGGCGCCACCGAGTGGCGCCCCAAGAACGCCGGCGCCAACGGCGCCATCTCCACCGGCAAGACCAGCAACGGCAACTCCGTGTCCATGTGA SEQ ID NO: 50Prototheca moriformis (UTEX 1435) KAS1 allele 1 5′ donor sequencegctcttcctcaccgcgtgaattgctgtcccaaacgtaagcatcatcgtggctcggtcacgcgatcctggatccggggatcctagaccgctggtggagagcgctgccgtcggattggtggcaagtaagattgcgcaggttggcgaagggagagaccaaaaccggaggctggaagcgggcacaacatcgtattattgcgtatagtagagcagtggcagtcgcatttcgaggtccgcaacggatctcgcaagctcgctacgctcacagtaggagaaaggggaccactgcccctgccagaatggtcgcgaccctctccctcgccggccccgcctgcaacacgcagtgcgtatccggcaagcgggctgtcgccttcaaccgcccccatgttggcgtccgggctcgatcaggtgcgctgaggggggtttggtgtgcccgcgcctctgggcccgtgtcggccgtgcggacgtggggccctgggcagtggatcagcagggtttgcgtgcaaatgcctataccggcgattgaatagcgatgaacgggatacggttgcgctcactccatgcccatgcgaccccgtttctgtccgccagccgtggtcgcccgggctgcgaagcgggaccccacccagcgcattgtgatcaccggaatgggcgtgggtacc SEQ ID NO: 51Prototheca moriformis (UTEX 1435) KAS1 allele 1 3′ donor sequencegagctccacctgcatccgcctggcgctcgaggacgccggcgtctcgcccgacgaggtcaactacgtcaacgcgcacgccacctccaccctggtgggcgacaaggccgaggtgcgcgcggtcaagtcggtctttggcgacatgaagggcatcaagatgaacgccaccaagtccatgatcgggcactgcctgggcgccgccggcggcatggaggccgtcgccacgctcatggccatccgcaccggctgggtgcaccccaccatcaaccacgacaaccccatcgccgaggtcgacggcctggacgtcgtcgccaacgccaaggcccagcacaaaatcaacgtcgccatctccaactccttcggcttcggcgggcacaactccgtcgtcgcctttgcgcccttccgcgagtaggcggagcgagcgcgcttggctgaggagggaggcggggtgcgagccctttggctgcgcgcgatactctccccgcacgagcagactccacgcgcctgaatctacttgtcaacgagcaaccgtgtgttttgtccgtggccattcttattatttctccgactgtggccgtactctgtttggctgtgcaagcaccgaagagccSEQ ID NO: 52 Prototheca moriformis (UTEX 1435) KAS1 allele 2 5′donor sequencegctcttcgcgcaagctcgctacgctcacagtaggagataggggaccactgcccctgccagaatggtcgcgaccctgtccctcgccggccccgcctgcaacacgcagtgcgtatccagcaagcgggttgtcgccttcaaccgcccccatgttggcgtccgggctcgatcaggtgcgctgaggggggtttggtgggcccgcgcctctgggcccgtgtcggccgtgcggacgtggggcccggggtagtggatcagcaggggttgcatgcaaatgcctataccggcgattgaatagcgatgaacgggatacggttgcgctcactccatgcccatgcgaccccgtttctgtccgccagccgtggtcgcccgagctgcgaagcgggaccccacccagcgcattgtgatcaccggaatgggcgtggcctccgtgtttggcaacgatgtcgagaccttttacgacaagcttctggaaggaacgagcggcgtggacctgatttccaggtgcgtaggtccttggatgaatgcgtctaggttgcgaggtgactggccaggaagcagcaggcttggggtttggtgttctgatttctggtaatttgaggtttcattataagattctgtacggtcttgtttcggggtacc SEQ ID NO: 53Prototheca moriformis (UTEX 1435) KAS1 allele 2 3′ donor sequencegagctccacctgcatccgcctggcgctcgaggacgccggcgtctcgcccgacgaggtcaactacgtcaacgcgcacgccacctccaccctggtgggcgacaaggccgaggtgcgcgcggtcaagtcggtctttggcgacatgaagggcatcaagatgaacgccaccaagtccatgatcgggcactgcctgggcgccgccggcggcatggaggccgtcgccacgctcatggccatccgcaccggctgggtgcaccccaccatcaaccacgacaaccccatcgccgaggtcgacggcctggacgtcgtcgccaacgccaaggcccagcacaaaatcaacgtcgccatctccaactccttcggcttcggcgggcacaactccgtcgtcgcctttgcgcccttccgcgagtaggcggagcgagcgcgcttggctgaggagggaggcggggtgcgagccctttggctgcgcgcgatactctccccgcacgagcagactccacgcgcctgaatctacttgtcaacgagcaaccgtgtgttttgtccgtggccattcttattatttctccgactgtggccgtactctgtttggctgtgcaagcaccgaagagccSEQ ID NO: 54 Prototheca moriformis (UTEX 1435) KSI-hairpin BactagtcaTGGTCGCCCGGGCTGCGAAGCGGGACCCCACCCAGCGCATTGTGATCACCGGAATGGGCGTGGCCTCCGTGTTTGGCAACGATGTCGAGACCTTTTACAgtgtgtttgagggttttggttgcccgtattgaggtcctggtggcgcgcatggaggagaaggcgcctgtcccgctgacccccccggctaccctcccggcaccttccagggcgcgtacgggatccTGTAAAAGGTCTCGACATCGTTGCCAAACACGGAGGCCACGCCCATTCCGGTGATCACAATGCGCTGGGTGGGGTCCCGCTTCGCAGCCCGGGCGACCAaagcttSEQ ID NO: 55 Prototheca moriformis (UTEX 1435) KSI-hairpin CactagtcaTTGACATCTCCGAGTTCCCGACCAAGTTTGCGGCGCAGATCACCGGCTTCTCCGTGGAGGACTGCGTGGACAAGAAGAACGCGCGGCGGTACGACGACGCGCTGTCGTACGCGATGGTGGCCTCCAAGAAGGCCCTGCGCCAGGCGGGACTGGAGAAGGACAAGTGCCCCGAGGGCTACGGAGgtgtgtttgagggttttggttgcccgtattgaggtcctggtggcgcgcatggaggagaaggcgcctgtcccgctgacccccccggctaccctcccggcaccttccagggcgcgtacgggatccCTCCGTAGCCCTCGGGGCACTTGTCCTTCTCCAGTCCCGCCTGGCGCAGGGCCTTCTTGGAGGCCACCATCGCGTACGACAGCGCGTCGTCGTACCGCCGCGCGTTCTTCTTGTCCACGCAGTCCTCCACGGAGAAGCCGGTGATCTGCGCCGCAAACTTGGTCGGGAACTCGGAGATGTCAAaagctt SEQ ID NO: 56Prototheca moriformis (UTEX 1435) KSI-hairpin DactagtcaTGGGCGTGAGCACCTGCATCCGCCTGGCGCTCGAGGACGCCGGCGTCTCGCCCGACGAGGTCAACTACGTCAACGCGCACGCCACCTCCACCCTGGTGGGCGACAAGGCCGAGGTGCGCGCGGTCAAGTCGGTCTTTGGCGACATGAAGGGCATCAAGATgtgtgtttgagggttttggttgcccgtattgaggtcctggtggcgcgcatggaggagaaggcgcctgtcccgctgacccccccggctaccctcccggcaccttccagggcgcgtacgggatccATCTTGATGCCCTTCATGTCGCCAAAGACCGACTTGACCGCGCGCACCTCGGCCTTGTCGCCCACCAGGGTGGAGGTGGCGTGCGCGTTGACGTAGTTGACCTCGTCGGGCGAGACGCCGGCGTCCTCGAGCGCCAGGCGGATGCAGGTGCTCACGCCCAaagctt SEQ ID NO: 57Prototheca moriformis (UTEX 1435) KSI-hairpin EactagtcaCAACCATCAACCACGACAACCCCATCGCCGAGGTCGACGGCCTGGACGTCGTCGCCAACGCCAAGGCCCAGCACAAAATCAACGTCGCCATCTCCAACTCCTTCGgtgtgtttgagggttttggttgcccgtattgaggtcctggtggcgcgcatggaggagaaggcgcctgtcccgctgacccccccggctaccctcccggcaccttccagggcgcgtacgggatccCGAAGGAGTTGGAGATGGCGACGTTGATTTTGTGCTGGGCCTTGGCGTTGGCGACGACGTCCAGGCCGTCGACCTCGGCGATGGGGTTGTCGTGGTTGATGGTaagctt SEQ ID NO: 58Codon optimized M. polymorpha FAE3 (GenBank Accession No. AAP74370)ATGgactcccgcgcccagaaccgcgacggcggcgaggacgtgaagcaggagctgctgtccgccggcgacgacggcaaggtgccctgccccaccgtggccatcggcatccgccagcgcctgcccgacttcctgcagtccgtgaacatgaagtacgtgaagctgggctaccactacctgatcacccacgccatgttcctgctgaccctgcccgccttcttcctggtggccgccgagatcggccgcctgggccacgagcgcatctaccgcgagctgtggacccacctgcacctgaacctggtgtccatcatggcctgctcctccgccctggtggccggcgccaccctgtacttcatgtcccgcccccgccccgtgtacctggtggagttcgcctgctaccgccccgacgagcgcctgaaggtgtccaaggacttcttcctggacatgtcccgccgcaccggcctgttctcctcctcctccatggacttccagaccaagatcacccagcgctccggcctgggcgacgagacctacctgccccccgccatcctggcctccccccccaacccctgcatgcgcgaggcccgcgaggaggccgccatggtgatgttcggcgccctggacgagctgttcgagcagaccggcgtgaagcccaaggagatcggcgtgctggtggtgaactgctccctgttcaaccccaccccctccatgtccgccatgatcgtgaaccactaccacatgcgcggcaacatcaagtccctgaacctgggcggcatgggctgctccgccggcctgatctccatcgacctggcccgcgacctgctgcaggtgcacggcaacacctacgccgtggtggtgtccaccgagaacatcaccctgaactggtacttcggcgacgaccgctccaagctgatgtccaactgcatcttccgcatgggcggcgccgccgtgctgctgtccaacaagcgccgcgagcgccgccgcgccaagtacgagctgctgcacaccgtgcgcacccacaagggcgccgacgacaagtgcttccgctgcgtgtaccaggaggaggactccaccggctccctgggcgtgtccctgtcccgcgagctgatggccgtggccggcaacgccctgaaggccaacatcaccaccctgggccccctggtgctgcccctgtccgagcagatcctgttcttcgcctccctggtggcccgcaagttcctgaacatgaagatgaagccctacatccccgacttcaagctggccttcgagcacttctgcatccacgccggcggccgcgccgtgctggacgagctggagaagaacctggacctgaccgagtggcacatggagccctcccgcatgaccctgtaccgcttcggcaacacctcctcctcctccctgtggtacgagctggcctacaccgaggcccagggccgcgtgaagcgcggcgaccgcctgtggcagatcgccttcggctccggcttcaagtgcaactccgccgtgtggcgcgcgctgcgcaccgtgaagccccccgtgaacaacgcctggtccgacgtgatcgaccgcttccccgtgaagctgccccagttcTGA SEQ ID NO: 59M. polymorpha FAE3 (GenBank Accession No. AAP74370)MDSRAQNRDGGEDVKQELLSAGDDGKVPCPTVAIGIRQRLPDFLQSVNMKYVKLGYHYLITHAMFLLTLPAFFLVAAEIGRLGHERIYRELWTHLHLNLVSIMACSSALVAGATLYFMSRPRPVYLVEFACYRPDERLKVSKDFFLDMSRRTGLFSSSSMDFQTKITQRSGLGDETYLPPAILASPPNPCMREAREEAAMVMFGALDELFEQTGVKPKEIGVLVVNCSLFNPIPSMSAMIVNHYHMRGNIKSLNLGGMGCSAGLISIDLARDLLQVHGNIYAVVVSTENITLNWYFGDDRSKLMSNCIFRMGGAAVLLSNKRRERRRAKYELLHIVRTHKGADDKCFRCVYQEEDSIGSLGVSLSRELMAVAGNALKANITTLGPLVLPLSEQILFFASLVARKFLNMKMKPYIPDFKLAFEHFCIHAGGRAVLDELEKNLDLTEWHMEPSRMTLYRFGNISSSSLWYELAYTEAQGRVKRGDRLWQIAFGSGFKCNSAVWRALRIVKPPVNNAWSDVIDRFPVKLPQF SEQ ID NO: 60Trypanosoma brucei ELO3 (GenBank Accession No. AAX70673)

gtggatgctggaccacccctccgtgccctacatcgccggcgtgatgtacctgatcctggtgctgtacgtgcccaagtccatcatggcctcccagccccccctgaacctgcgcgccgccaacatcgtgtggaacctgttcctgaccctgttctccatgtgcggcgcctactacaccgtgccctacctggtgaaggccttcatgaaccccgagatcgtgatggccgcctccggcatcaagctggacgccaacacctcccccatcatcacccactccggcttctacaccaccacctgcgccctggccgactccttctacttcaacggcgacgtgggcttctgggtggccctgttcgccctgtccaagatccccgagatgatcgacaccgccttcctggtgttccagaagaagcccgtgatcttcctgcactggtaccaccacctgaccgtgatgctgttctgctggttcgcctacgtgcagaagatctcctccggcctgtggttcgcctccatgaactactccgtgcactccatcatgtacctgtactacttcgtgtgcgcctgcggccaccgccgcctggtgcgccccttcgcccccatcatcaccttcgtgcagatcttccagatggtggtgggcaccatcgtggtgtgctacacctacaccgtgaagcacgtgctgggccgctcctgcaccgtgaccgacttctccctgcacaccggcctggtgatgtacgtgtcctacctgctgctgttctcccagctgttctaccgctcctacctgtccccccgcgacaaggcctccatcccccacgtggccgc

SEQ ID NO: 61 Trypanosoma brucei ELO3 (GenBank Accession No. AAX70673)MYPTHRDLILNNYSDIYRSPTCHYHTWHTLIHTPINELLFPNLPRECDFGYDIPYFRGQIDVFDGWSMIHFTSSNWCIPITVCLCYIMMIAGLKKYMGPRDGGRAPIQAKNYIIAWNLFLSFFSFAGVYYTVPYHLFDPENGLFAQGFYSTVCNNGAYYGNGNVGFFVWLFIYSKIFELVDIFFLLIRKNPVIFLHWYHHLTVLLYCWHAYSVRIGIGIWFATMNYSVHSVMYLYFAMTQYGPSTKKFAKKFSKFITTIQILQMVVGIIVTFAAMLYVTFDVPCYTSLANSVLGLMMYASYFVLFVQLYVSHYVSPKHVKQE SEQ ID NO: 62Codon optimized Saccharomyces cerevisiae ELO1 (GenBank Accession No.P39540)

cttcttcaacatctacctgtgggactacttcaaccgcgccgtgggctgggccaccgccggccgcttccagcccaaggacttcgagttcaccgtgggcaagcagcccctgtccgagccccgccccgtgctgctgttcatcgccatgtactacgtggtgatcttcggcggccgctccctggtgaagtcctgcaagcccctgaagctgcgcttcatctcccaggtgcacaacctgatgctgacctccgtgtccttcctgtggctgatcctgatggtggagcagatgctgcccatcgtgtaccgccacggcctgtacttcgccgtgtgcaacgtggagtcctggacccagcccatggagaccctgtactacctgaactacatgaccaagttcgtggagttcgccgacaccgtgctgatggtgctgaagcaccgcaagctgaccttcctgcacacctaccaccacggcgccaccgccctgctgtgctacaaccagctggtgggctacaccgccgtgacctgggtgcccgtgaccctgaacctggccgtgcacgtgctgatgtactggtactacttcctgtccgcctccggcatccgcgtgtggtggaaggcctgggtgacccgcctgcagatcgtgcagttcatgctggacctgatcgtggtgtactacgtgctgtaccagaagatcgtggccgcctacttcaagaacgcctgcaccccccagtgcgaggactgcctgggctccatgaccgccatcgccgccggcgccgccatcctgacctcctacctgttcctgttcatctccttctacatcgaggtgta

SEQ ID NO: 63Saccharomyces cerevisiae ELO1 (GenBank Accession No. P39540)MVSDWKNFCLEKASRFRPTIDRPFFNIYLWDYFNRAVGWATAGRFQPKDFEFTVGKQPLSEPRPVLLFIAMYYVVIFGGRSLVKSCKPLKLRFISQVHNLMLTSVSFLWLILMVEQMLPIVYRHGLYFAVCNVESWTQPMETLYYLNYMTKFVEFADTVLMVLKHRKLTFLHTYHHGATALLCYNQLVGYTAVTWVPVTLNLAVHVLMYWYYFLSASGIRVWWKAWVTRLQIVQFMLDLIVVYYVLYQKIVAAYFKNACTPQCEDCLGSMTAIAAGAAILTSYLFLFISFYIEVYKRGSASGKKKINKNN SEQ ID NO: 64Codon optimized Brassica napus acyl-ACP thioesterase (GenBankAccession No. CAA52070) with 3X FLAG TagATGctgaagctgtcctgcaacgtgaccaacaacctgcacaccttctccttcttctccgactcctccctgttcatccccgtgaaccgccgcaccatcgccgtgtcctccgggcgcgcctcccagctgcgcaagcccgccctggaccccctgcgcgccgtgatctccgccgaccagggctccatctcccccgtgaactcctgcacccccgccgaccgcctgcgcgccggccgcctgatggaggacggctactcctacaaggagaagttcatcgtgcgctcctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtggcctgcaaccacgtgcagaagtgcggcttctccaccgacggcttcgccaccaccctgaccatgcgcaagctgcacctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtggtggagatcgagacctggtgccagtccgagggccgcatcggcacccgccgcgactggatcctgcgcgactccgccaccaacgaggtgatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagcgcgtgaccgacgaggtgcgcgacgagtacctggtgttctgcccccgcgagccccgcctggccttccccgaggagaacaactcctccctgaagaagatccccaagctggaggaccccgcccagtactccatgctggagctgaagccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatcccccaggagatcatcgacacccacgagctgcaggtgatcaccctggactaccgccgcgagtgccagcaggacgacatcgtggactccctgaccacctccgagatccccgacgaccccatctccaagttcaccggcaccaacggctccgccatgtcctccatccagggccacaacgagtcccagttcctgcacatgctgcgcctgtccgagaacggccaggagatcaaccgcggccgcacccagtggcgcaagaagtoctoccgcATGGACTACAAGGACCACGACGGCGACTACAAGGACCACGACATCGACTACAAGGACGACGACGACAAGTGA SEQ ID NO: 65Brassica napus acyl-ACP thioesterase (Genbank Accession No.CAA52070) with 3X FLAG Tag (bold)

PADRLRAGRLMEDGYSYKEKFIVRSYEVGINKTATVETIANLLQEVACNHVQKCGFSTDGFATTLTMRKLHLIWVTARMHIETYKYPAWSDVVEIETWCQSEGRIGTRRDWILRDSATNEVIGRATSKWVMMNQDTRRLQRVTDEVRDEYLVFCPREPRLAFFEENNSSLKKIPKLEDPAQYSMLELKPRRADLDMNQHVNNVTYIGWVLESIPQEIIDTHELQVITLDYRRECQQDDIVDSLTTSEIPDDPISKFTGTNGSAMSSIQGHNESQFLHMLRLSENGQEINRGRTQWRKKSSRMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 66Codon optimized Brassica napus acyl-ACP thioesterase (GenBankAccession No. CAA52070), with UTEX 250 stearoyl-ACP desaturase (SAD)chloroplast transit peptide and 3X FLAG TagATGgccaccgcatccactttctcggcgttcaatgcccgctgcggcgacctgcgtcgctcggcgggctccgggccccggcgcccagcgaggcccctccccgtgcgcgggcgcgcctcccagctgcgcaagcccgccctggaccccctgcgcgccgtgatctccgccgaccagggctccatctcccccgtgaactcctgcacccccgccgaccgcctgcgcgccggccgcctgatggaggacggctactcctacaaggagaagttcatcgtgcgctcctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtggcctgcaaccacgtgcagaagtgcggcttctccaccgacggcttcgccaccaccctgaccatgcgcaagctgcacctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtggtggagatcgagacctggtgccagtccgagggccgcatcggcacccgccgcgactggatcctgcgcgactccgccaccaacgaggtgatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagcgcgtgaccgacgaggtgcgcgacgagtacctggtgttctgcccccgcgagccccgcctggccttccccgaggagaacaactcctccctgaagaagatccccaagctggaggaccccgcccagtactccatgctggagctgaagccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatcccccaggagatcatcgacacccacgagctgcaggtgatcaccctggactaccgccgcgagtgccagcaggacgacatcgtggactccctgaccacctccgagatccccgacgaccccatctccaagttcaccggcaccaacggctccgccatgtcctccatccagggccacaacgagtcccagttcctgcacatgctgcgcctgtccgagaacggccaggagatcaaccgcggccgcacccagtggcgcaagaagtoctoccgcATGGACTACAAGGACCACGACGGCGACTACAAGGACCACGACATCGACTACAAGGACGACGACGACAAGTGA SEQ ID NO: 67Brassica napus acyl-ACP thioesterase (GenBank Accession No.CAA52070) with UTEX 250 stearoyl-ACP desaturase (SAD) chloroplasttransit peptide and 3X FLAG ® Tag

ADRLRAGRLMEDGYSYKEKFIVRSYEVGINKTATVETIANLLQEVACNHVQKCGFSTDGFATTLTMRKLHLIWVTARMHIETYKYPAWSDVVEIETWCQSEGRIGIRRDWILRDSATNEVIGRATSKWVMMNQDTRRLQRVTDEVRDEYLVFCPREPRLAFPEENNSSLKKIPKLEDPAQYSMLELKPRRADLDMNQHVNNVTYIGWVLESIPQEIIDTHELQVITLDYRRECQQDDIVDSLTTSEIPDDPISKFTGTNGSAMSSIQGHNESQFLHMLRLSENGQEINRGRTQWRKKSSRMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 68Codon optimized C. tinctorius FATA (GenBank Accession No. AAA33019)with UTEX 250 stearoyl-ACP desaturase (SAD) chloroplast transitpeptide and 3X FLAG ® Tag

gcgtggcctccctgcgcgaggccgacaaggagaagtccctgggcaaccgcctgcgcctgggctccctgaccgaggacggcctgtcctacaaggagaagttcgtgatccgctgctacgaggtgggcatcaacaagaccgccaccatcgagaccatcgccaacctgctgcaggaggtgggcggcaaccacgcccagggcgtgggcttctccaccgacggcttcgccaccaccaccaccatgcgcaagctgcacctgatctgggtgaccgcccgcatgcacatcgagatctaccgctaccccgcctggtccgacgtgatcgagatcgagacctgggtgcagggcgagggcaaggtgggcacccgccgcgactggatcctgaaggactacgccaacggcgaggtgatcggccgcgccacctccaagtgggtgatgatgaacgaggacacccgccgcctgcagaaggtgtccgacgacgtgcgcgaggagtacctggtgttctgcccccgcaccctgcgcctggccttccccgaggagaacaacaactccatgaagaagatccccaagctggaggaccccgccgagtactcccgcctgggcctggtgccccgccgctccgacctggacatgaacaagcacgtgaacaacgtgacctacatcggctgggccctggagtccatcccccccgagatcatcgacacccacgagctgcaggccatcaccctggactaccgccgcgagtgccagcgcgacgacatcgtggactccctgacctcccgcgagcccctgggcaacgccgccggcgtgaagttcaaggagatcaacggctccgtgtcccccaagaaggacgagcaggacctgtcccgcttcatgcacctgctgcgctccgccggctccggcctggagatcaaccgctgccgcaccgagtggcgcaagaagcccgccaagcgcATGGA

SEQ ID NO: 69C. tinctorius FATA (GenBank Accession No. AAA33019) with UTEX 250stearoyl-ACP desaturase (SAD) chloroplast transit peptide

TEDGLSYKEKFVIRCYEVGINKTATIETIANLLQEVGGNHAQGVGFSTDGFATTTTMRKLHLIWVTARMHIETYRYPAWSDVIEIETWVQGEGKVGTRRDWILKDYANGEVIGRATSKWVMMNEDTRRLQKVSDDVREEYLVFCPRTLRLAFPEENNNSMKKIPKLEDPAEYSRLGLVPRRSDLDMNKHVNNVTYIGWALESIPPEIIDTHELQAITLDYRRECQRDDIVDSLTSREPLGNAAGVKFKEINGSVSPKKDEQDLSRFMHLLRSAGSGLEINRCRIEWRKKPAKRMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 70Codon optimized R. communis FATA (Genbank Accession No. ABS30422)with a 3xFLAG epitope tag

gacccacttcaacaaccgcccctacttcacccgccgcccctccatccccaccttcttctcctccaagaactcctccgcctccctgcaggccgtggtgtccgacatctcctccgtggagtccgccgcctgcgactccctggccaaccgcctgcgcctgggcaagctgaccgaggacggcttctcctacaaggagaagttcatcgtggggcgcgcccgctcctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtgggctgcaaccacgcccagtccgtgggcttctccaccgacggcttcgccaccaccacctccatgcgcaagatgcacctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtggtggaggtggagacctggtgccagtccgagggccgcatcggcacccgccgcgactggatcctgaccgactacgccaccggccagatcatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagaaggtgaccgacgacgtgcgcgaggagtacctggtgttctgcccccgcgagctgcgcctggccttccccgaggagaacaaccgctcctccaagaagatctccaagctggaggaccccgcccagtactccaagctgggcctggtgccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatcccccaggagatcatcgacacccacgagctgcagaccatcaccctggactaccgccgcgagtgccagcacgacgacatcgtggactccctgacctccgtggagccctccgagaacctggaggccgtgtccgagctgcgcggcaccaacggctccgccaccaccaccgccggcgacgaggactgccgcaacttcctgcacctgctgcgcctgtccggcgacggcctggagatcaaccgcggccgcaccgagtggcgcaagaagtccgcccgcATGGACTACAAGGACCACGACGGCGACTACAAGG

SEQ ID NO: 71R. communis FATA (Genbank Accession No. AB530422) with a 3xFLAG ®epitope tag

SMRKMHLIWVTARMHIETYKYPAWSDVVEVETWCQSEGRIGIRRDWILTDYATGQIIGRATSKWVMMNQDTRRLQKVTDDVREEYLVFCPRELRLAFFEENNRSSKKISKLEDPAQYSKLGLVPRRADLDMNQHVNNVTYIGWVLESIPQEIIDTHELQTITLDYRRECQHDDIVDSLTSVEPSENLEAVSELRGTNGSATTTAGDEDCRNFLHLLRLSGDGLEINRGRIEWRKKSARMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 72Codon optimized G. mangostana FATA1 (GenBank Accession No. AAB51523)with 3X FLAG ® epitope tag

ccccccccgcatcatcgtggtgtcctcctcctcctccaaggtgaaccccctgaagaccgaggccgtggtgtcctccggcctggccgaccgcctgcgcctgggctccctgaccgaggacggcctgtcctacaaggagaagttcatcgtgcgctgctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtgggctgcaaccacgcccagtccgtgggctactccaccggcggcttctccaccacccccaccatgcgcaagctgcgcctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtggtggagatcgagtcctggggccagggcgagggcaagatcggcacccgccgcgactggatcctgcgcgactacgccaccggccaggtgatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagaaggtggacgtggacgtgcgcgacgagtacctggtgcactgcccccgcgagctgcgcctggccttccccgaggagaacaactcctccctgaagaagatctccaagctggaggacccctcccagtactccaagctgggcctggtgccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatgccccaggagatcatcgacacccacgagctgcagaccatcaccctggactaccgccgcgagtgccagcacgacgacgtggtggactccctgacctcccccgagccctccgaggacgccgaggccgtgttcaaccacaacggcaccaacggctccgccaacgtgtccgccaacgaccacggctgccgcaacttcctgcacctgctgcgcctgtccggcaacggcctggagatcaaccgcggccgcaccgagtggcgcaagaagcccacccgcATGGACTACAAGGACCACGACGGCGACTACAA

SEQ ID NO: 73G. mangostana FATA1 (GenBank Accession No. AAB51523) with 3X FLAG ®epitope tagMLKLSSSRSPLARIPTRPRPNSIPPRIIVVSSSSSKVNPLKTEAVVSSGLADRLRLGSLTEDGLSYKEKFIVRCYEVGINKTATVETIANLLQEVGCNHAQSVGYSIGGESTIPTMRKLRLIWVTARMHIETYKYPAWSDVVEIESWGQGEGKIGIRRDWILRDYATGQVIGRATSKWVMMNQDTRRLQKVDVDVRDEYLVHCPRELRLAFPEENNSSLKKISKLEDPSQYSKLGLVPRRADLDMNQHVNNVTYIGWVLESMPQEIIDTHELQTITLDYRRECQHDDVVDSLTSPEPSEDAEAVFNHNGTNGSANVSANDHGCRNFLHLLRLSGNGLEINRGRTEWRKKFTRMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 74Codon optimized Theobroma cacao FATA1 with 3X FLAG ® epitope tag

cccccccgcccccttctccttccgctggcgcacccccgtggtggtgtcctgctccccctcctcccgccccaacctgtcccccctgcaggtggtgctgtccggccagcagcaggccggcatggagctggtggagtccggctccggctccctggccgaccgcctgcgcctgggctccctgaccgaggacggcctgtcctacaaggagaagttcatcgtgcgctgctacgaggtgggcatcaacaagaccgccaccgtggagaccatcgccaacctgctgcaggaggtgggctgcaaccacgcccagtccgtgggctactccaccgacggcttcgccaccacccgcaccatgcgcaagctgcacctgatctgggtgaccgcccgcatgcacatcgagatctacaagtaccccgcctggtccgacgtgatcgagatcgagacctggtgccagtccgagggccgcatcggcacccgccgcgactggatcctgaaggacttcggcaccggcgaggtgatcggccgcgccacctccaagtgggtgatgatgaaccaggacacccgccgcctgcagaaggtgtccgacgacgtgcgcgaggagtacctggtgttctgcccccgcgagctgcgcctggccttccccgaggagaacaacaactccctgaagaagatcgccaagctggacgactccttccagtactcccgcctgggcctgatgccccgccgcgccgacctggacatgaaccagcacgtgaacaacgtgacctacatcggctgggtgctggagtccatgccccaggagatcatcgacacccacgagctgcagaccatcaccctggactaccgccgcgagtgccagcaggacgacgtggtggactccctgacctcccccgagcaggtggagggcaccgagaaggtgtccgccatccacggcaccaacggctccgccgccgcccgcgaggacaagcaggactgccgccagttcctgcacctgctgcgcctgtcctccgacggccaggagatcaaccgcggccgcaccgagtggcgcaagaagcccgcccgcATGGACTACAAGGACCACGACGGCGACTACA

SEQ ID NO: 75 Theobroma cacao FATA1 with 3X FLAG ® epitope tagMLKLSSCNVTDQRQALAQCRFLAPPAPFSFRWRTPVVVSCSPSSRPNLSPLQVVLSGQQQAGMELVESGSGSLADRLRLGSLTEDGLSYKEKFIVRCYEVGINKTATVETIANLLQEVGCNHAQSVGYSTDGFATTRTMRKLHLIWVTARMHIETYKYPAWSDVIEIETWCQSEGRIGTRRDWILKDFGTGEVIGRATSKWVMMNQDTRRLQKVSDDVREEYLVFCPRELRLAFPEENNNSLKKIAKLDDSFQYSRLGLMPRRADLDMNQHVNNVTYIGWVLESMPQEIIDTHELQTITLDYRRECQQDDVVDSLTSPEQVEGTEKVSAIHGTNGSAAAREDKQDCRQFLHLLRLSSDGQEINRGRTEWRKKPARMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 7623S rRNA for UTEX 1439, UTEX 1441, UTEX 1435, UTEX 1437 ProtothecamoriformisTGTTGAAGAATGAGCCGGCGACTTAAAATAAATGGCAGGCTAAGAGAATTAATAACTCGAAACCTAAGCGAAAGCAAGTCTTAATAGGGCGCTAATTTAACAAAACATTAAATAAAATCTAAAGTCATTTATTTTAGACCCGAACCTGAGTGATCTAACCATGGTCAGGATGAAACTTGGGTGACACCAAGTGGAAGTCCGAACCGACCGATGTTGAAAAATCGGCGGATGAACTGTGGTTAGTGGTGAAATACCAGTCGAACTCAGAGCTAGCTGGTTCTCCCCGAAATGCGTTGAGGCGCAGCAATATATCTCGTCTATCTAGGGGTAAAGCACTGTTTCGGTGCGGGCTATGAAAATGGTACCAAATCGTGGCAAACTCTGAATACTAGAAATGACGATATATTAGTGAGACTATGGGGGATAAGCTCCATAGTCGAGAGGGAAACAGCCCAGACCACCAGTTAAGGCCCCAAAATGATAATGAAGTGGTAAAGGAGGTGAAAATGCAAATACAACCAGGAGGTTGGCTTAGAAGCAGCCATCCTTTAAAGAGTGCGTAATAGCTCACTG SEQ ID NO: 77 Cu P5R23 LPAAT2-1MAIAAAAVIFLFGLIFFASGLIINLFQALCFVLIRPLSKNAYRRINRVFAELLLSELLCLFDWWAGAKLKLFTDPETFRLMGKEHALVIINHMTELDWMVGWVMGQHFGCLGSIISVAKKSTKFLPVLGWSMWFSEYLYLERSWAKDKSTLKSHIERLIDYPLPFWLVIFVEGTRFTRTKLLAAQQYAVSSGLPVPRNVLIPRTKGFVSCVSHMRSFVPAVYDVTVAFPKTSPPPTLLNLFEGQSIMLHVHIKRHAMKDLPESDDAVAEWCRDKFVEKDALLDKHNAEDTFSGQEVCHSGSRQLKSLLVVISWVVVTTFGALKFLQWSSWKGKAFSAIGLGIVTLLMHVLILSSQAERSNPAEVAQAKLKTGLSISKKVTDKEN SEQ ID NO: 78CuPSR23 LPAAT3-1MAIAAAAVIVPLSLLFFVSGLIVNLVQAVCFVLIRPLSKNTYRRINRVVAELLWLELVWLIDWWAGVKIKVFTDHETFHLMGKEHALVICNHKSDIDWLVGWVLGQRSGCLGSTLAVMKKSSKFLPVLGWSMWFSEYLFLERSWAKDEITLKSGLNRLKDYPLPFWLALFVEGTRFTRAKLLAAQQYAASSGLPVPRNVLIPRTKGFVSSVSHMRSFVPAIYDVIVAIPKTSPPPTLIRMFKGQSSVLHVHLKRHLMKDLPESDDAVAQWCRDIFVEKDALLDKHNAEDTFSGQELQETGRPIKSLLVVISWAVLEVFGAVKFLQWSSLLSSWKGLAFSGIGLGVITLLMHILILFSQSERSTPAKVAPAKPKNEGESSKTEMEKEK SEQ ID NO: 79Amino acid sequence for CuPSR23 LPPATxMEIPPHCLCSPSPAPSQLYYKKKKHAILQTQTPYRYRVSPTCFAPPRLRKQHPYPLPVLCYPKLLHFSQPRYPLVRSHLAEAGVAYRPGYELLGKIRGVCFYAVTAAVALLLFQCMLLLHPFVLLFDPFPRKAHHTIAKLWSICSVSLFYKIHIKGLENLPPPHSPAVYVSNHQSFLDIYTLLTLGRTFKFISKTEIFLYPIIGWAMYMLGTIPLKRLDSRSQLDTLKRCMDLIKKGASVFFFPEGTRSKDGKLGAFKKGAFSIAAKSKVPVVPITLIGTGKIMPPGSELTVNPGTVQVIIHKPIEGSDAEAMCNEARATISHSLDD SEQ ID NO: 80cDNA sequence for CuPSR23 LPAATx coding regionATGGAGATCCCGCCTCACTGTCTCTGTTCGCCTTCGCCTGCGCCTTCGCAATTGTATTACAAGAAGAAGAAGCATGCCATTCTCCAAACTCAAACTCCCTATAGATATAGAGTTTCCCCGACATGCTTTGCCCCCCCCCGATTGAGGAAGCAGCATCCTTACCCTCTCCCTGTCCTCTGCTATCCAAAACTCCTCCACTTCAGCCAGCCTAGGTACCCTCTGGTTAGATCTCATTTGGCTGAAGCTGGTGTTGCTTATCGTCCAGGATACGAATTATTAGGAAAAATAAGGGGAGTGTGTTTCTATGCTGTCACTGCTGCCGTTGCCTTGCTTCTATTTCAGTGCATGCTCCTCCTCCATCCCTTTGTGCTCCTCTTCGATCCATTTCCAAGAAAGGCTCACCATACCATCGCCAAACTCTGGTCTATCTGCTCTGTTTCTCTTTTTTACAAGATTCACATCAAGGGTTTGGAAAATCTTCCCCCACCCCACTCTCCTGCCGTCTATGTCTCTAATCATCAGAGTTTTCTCGACATCTATACTCTCCTCACTCTCGGTAGAACCTTCAAGTTCATCAGCAAGACTGAGATCTTTCTCTATCCAATTATCGGTTGGGCCATGTATATGTTGGGTACCATTCCTCTCAAGCGGTTGGACAGCAGAAGCCAATTGGACACTCTTAAGCGATGTATGGATCTCATCAAGAAGGGAGCATCCGTCTTTTTCTTCCCAGAGGGAACACGAAGTAAAGATGGGAAACTGGGTGCTTTCAAGAAAGGTGCATTCAGCATCGCAGCAAAAAGCAAGGTTCCTGTTGTGCCGATCACCCTTATTGGAACTGGCAAGATTATGCCACCTGGGAGCGAACTTACTGTCAATCCAGGAACTGTGCAAGTAATCATACATAAACCTATCGAAGGAAGTGATGCAGAAGCAATGTGCAATGAAGCTAGAGCCACGATTTCTCACTCACTTGATGATTAA SEQ ID NO: 81cDNA sequence for CuPSR23 LPAAT 2-1 coding regionATGGCGATTGCAGCGGCAGCTGTCATCTTCCTCTTCGGCCTTATCTTCTTCGCCTCCGGCCTCATAATCAATCTCTTCCAGGCGCTTTGCTTTGTCCTTATTCGGCCTCTTTCGAAAAACGCCTACMGGAGAATAAACAGAGTTTTTGCAGAATTGTTGTTGTCGGAGCTTTTATGCCTATTCGATTGGTGGGCTGGTGCTAAGCTCAAATTATTTACCGACCCTGAAACCTTTCGCCTTATGGGCAAGGAACATGCTCTTGTCATAATTAATCACATGACTGAACTTGACTGGATGGTTGGATGGGTTATGGGTCAGCATTTTGGTTGCCTTGGGAGCATAATATCTGTTGCGAAGAAATCAACAAAATTTCTTCCGGTATTGGGGTGGTCAATGTGGTTTTCAGAGTACCTATATCTTGAGAGAAGCTGGGCCAAGGATAAAAGTACATTAAAGTCACATATCGAGAGGCTGATAGACTACCCCCTGCCCTTCTGGTTGGTAATTTTTGTGGAAGGAACTCGGTTTACTCGGACAAAACTCTTGGCAGCCCAGCAGTATGCTGTCTCATCTGGGCTACCAGTGCCGAGAAATGTTTTGATCCCACGTACTAAGGGTTTTGTTTCATGTGTAAGTCACATGCGATCATTTGTTCCAGCAGTATATGATGTCACAGTGGCATTCCCTAAGACTTCACCTCCACCAACGTTGCTAAATCTTTTCGAGGGTCAGTCCATAATGCTTCACGTTCACATCAAGCGACATGCAATGAAAGATTTACCAGAATCCGATGATGCAGTAGCAGAGTGGTGTAGAGACAAATTTGTGGAAAAGGATGCTTTGTTGGACAAGCATAATGCTGAGGACACTTTCAGTGGTCAAGAAGTTTGTCATAGCGGCAGCCGCCAGTTAAAGTCTCTTCTGGTGGTAATATCTTGGGTGGTTGTAACAACATTTGGGGCTCTAAAGTTCCTTCAGTGGTCATCATGGAAGGGGAAAGCATTTTCAGCTATCGGGCTGGGCATCGTCACTCTACTTATGCACGTATTGATTCTATCCTCACAAGCAGAGCGGTCTAACCCTGCGGAGGTGGCACAGGCAAAGCTAAAGACCGGGTTGTCGATCTCAAAGAAGGTAACGGACAAGGAAAACTAGSEQ ID NO: 82 cDNA sequence for CuPSR23 LPAAx 3-1 coding regionATGGCGATTGCTGCGGCAGCTGTCATCGTCCCGCTCAGCCTCCTCTTCTTCGTCTCCGGCCTCATCGTCAATCTCGTACAGGCAGTTTGCTTTGTACTGATTAGGCCTCTGTCGAAAAACACTTACAGAAGAATAAACAGAGTGGTTGCAGAATTGTTGTGGTTGGAGTTGGTATGGCTGATTGATTGGTGGGCTGGTGTCAAGATAAAAGTATTCACGGATCATGAAACCTTTCACCTTATGGGCAAAGAACATGCTCTTGTCATTTGTAATCACAAGAGTGACATAGACTGGCTGGTTGGGTGGGTTCTGGGACAGCGGTCAGGTTGCCTTGGAAGCACATTAGCTGTTATGAAGAAATCATCAAAGTTTCTCCCGGTATTAGGGTGGTCAATGTGGTTCTCAGAGTATCTATTCCTTGAAAGAAGCTGGGCCAAGGATGAAATTACATTAAAGTCAGGTTTGAATAGGCTGAAAGACTATCCCTTACCCTTCTGGTTGGCACTTTTTGTGGAAGGAACTCGGTTCACTCGAGCAAAACTCTTGGCAGCCCAGCAGTATGCTGCCTCTTCGGGGCTACCTGTGCCGAGAAATGTTCTGATCCCGCGTACTAAGGGTTTTGTTTCTTCTGTGAGTCACATGCGATCATTTGTTCCAGCCATATATGATGTTACAGTGGCAATCCCAAAGACGTCACCTCCACCAACATTGATAAGAATGTTCAAGGGACAGTCCTCAGTGCTTCACGTCCACCTCAAGCGACACCTAATGAAAGATTTACCTGAATCAGATGATGCTGTTGCTCAGTGGTGCAGAGATATATTCGTCGAGAAGGATGCTTTGTTGGATAAGCATAATGCTGAGGACACTTTCAGTGGCCAAGAACTTCAAGAAACTGGCCGCCCAATAAAGTCTCTTCTGGTTGTAATCTCTTGGGCGGTGTTGGAGGTATTTGGAGCTGTGAAGTTTCTTCAATGGTCATCGCTGTTATCATCATGGAAGGGACTTGCATTTTCGGGAATAGGACTGGGTGTCATCACGCTACTCATGCACATACTGATTTTATTCTCACAATCCGAGCGGTCTACCCCTGCAAAAGTGGCACCAGCAAAGCCAAAGAATGAGGGAGAGTCCTCCAAGACGGAAATGGAAAAGGAAAAGTAG SEQ ID NO: 83cDNA sequence for CuPSR23 LPAATx coding region codon optimized forPrototheca moriformisATGgagatccccccccactgcctgtgctccccctcccccgccccctcccagctgtactacaagaagaagaagcacgccatcctgcagacccagaccccctaccgctaccgcgtgtcccccacctgcttcgcccccccccgcctgcgcaagcagcacccctaccccctgcccgtgctgtgctaccccaagctgctgcacttctcccagccccgctaccccctggtgcgctcccacctggccgaggccggcgtggcctaccgccccggctacgagctgctgggcaagatccgcggcgtgtgcttctacgccgtgaccgccgccgtggccctgctgctgttccagtgcatgctgctgctgcaccccttcgtgctgctgttcgaccccttcccccgcaaggcccaccacaccatcgccaagctgtggtccatctgctccgtgtccctgttctacaagatccacatcaagggcctggagaacctgccccccccccactcccccgccgtgtacgtgtccaaccaccagtccttcctggacatctacaccctgctgaccctgggccgcaccttcaagttcatctccaagaccgagatcttcctgtaccccatcatcggctgggccatgtacatgctgggcaccatccccctgaagcgcctggactcccgctcccagctggacaccctgaagcgctgcatggacctgatcaagaagggcgcctccgtgttcttcttccccgagggcacccgctccaaggacggcaagctgggcgccttcaagaagggcgccttctccatcgccgccaagtccaaggtgcccgtggtgcccatcaccctgatcggcaccggcaagatcatgccccccggctccgagctgaccgtgaaccccggcaccgtgcaggtgatcatccacaagcccatcgagggctccgacgccgaggccatgtgcaacgaggcccgcgccaccatctcccactccctggacgacTGA SEQ ID NO: 84cDNA sequence for CuPSR23 LPAAT 2-1 coding region codon optimizedfor Prototheca moriformisATGgcgatcgcggccgcggcggtgatcttcctgttcggcctgatcttcttcgcctccggcctgatcatcaacctgttccaggcgctgtgcttcgtcctgatccgccccctgtccaagaacgcctaccgccgcatcaaccgcgtgttcgcggagctgctgctgtccgagctgctgtgcctgttcgactggtgggcgggcgcgaagctgaagctgttcaccgaccccgagacgttccgcctgatgggcaaggagcacgccctggtcatcatcaaccacatgaccgagctggactggatggtgggctgggtgatgggccagcacttcggctgcctgggctccatcatctccgtcgccaagaagtccacgaagttcctgcccgtgctgggctggtccatgtggttctccgagtacctgtacctggagcgctcctgggccaaggacaagtccaccctgaagtcccacatcgagcgcctgatcgactaccccctgcccttctggctggtcatcttcgtcgagggcacccgcttcacgcgcacgaagctgctggcggcccagcagtacgcggtctcctccggcctgcccgtcccccgcaacgtcctgatcccccgcacgaagggcttcgtctcctgcgtgtcccacatgcgctccttcgtccccgcggtgtacgacgtcacggtggcgttccccaagacgtcccccccccccacgctgctgaacctgttcgagggccagtccatcatgctgcacgtgcacatcaagcgccacgccatgaaggacctgcccgagtccgacgacgccgtcgcggagtggtgccgcgacaagttcgtcgagaaggacgccctgctggacaagcacaacgcggaggacacgttctccggccaggaggtgtgccactccggctcccgccagctgaagtccctgctggtcgtgatctcctgggtcgtggtgacgacgttcggcgccctgaagttcctgcagtggtcctcctggaagggcaaggcgttctccgccatcggcctgggcatcgtcaccctgctgatgcacgtgctgatcctgtcctcccaggccgagcgctccaaccccgccgaggtggcccaggccaagctgaagaccggcctgtccatctccaagaaggtgacggacaaggagaacTGASEQ ID NO: 85cDNA sequence for CuPSR23 LPAAx 3-1 coding region codon optimizedfor Prototheca moriformisATGgccatcgcggcggccgcggtgatcgtgcccctgtccctgctgttcttcgtgtccggcctgatcgtcaacctggtgcaggccgtctgcttcgtcctgatccgccccctgtccaagaacacgtaccgccgcatcaaccgcgtggtcgcggagctgctgtggctggagctggtgtggctgatcgactggtgggcgggcgtgaagatcaaggtcttcacggaccacgagacgttccacctgatgggcaaggagcacgccctggtcatctgcaaccacaagtccgacatcgactggctggtcggctgggtcctgggccagcgctccggctgcctgggctccaccctggcggtcatgaagaagtcctccaagttcctgcccgtcctgggctggtccatgtggttctccgagtacctgttcctggagcgctcctgggccaaggacgagatcacgctgaagtccggcctgaaccgcctgaaggactaccccctgcccttctggctggcgctgttcgtggagggcacgcgcttcacccgcgcgaagctgctggcggcgcagcagtacgccgcgtcctccggcctgcccgtgccccgcaacgtgctgatcccccgcacgaagggcttcgtgtcctccgtgtcccacatgcgctccttcgtgcccgcgatctacgacgtcaccgtggccatccccaagacgtcccccccccccacgctgatccgcatgttcaagggccagtcctccgtgctgcacgtgcacctgaagcgccacctgatgaaggacctgcccgagtccgacgacgccgtcgcgcagtggtgccgcgacatcttcgtggagaaggacgcgctgctggacaagcacaacgccgaggacaccttctccggccaggagctgcaggagaccggccgccccatcaagtccctgctggtcgtcatctcctgggccgtcctggaggtgttcggcgccgtcaagttcctgcagtggtcctccctgctgtcctcctggaagggcctggcgttctccggcatcggcctgggcgtgatcaccctgctgatgcacatcctgatcctgttctcccagtccgagcgctccacccccgccaaggtggcccccgcgaagcccaagaacgagggcgagtcctccaagaccgagatggagaaggagaagTGA SEQ ID NO: 86Nucleic acid sequence encoding 14:0-ACP thioesterase, Cupheapalustris (Cpal FATB2, accession AAC49180) containing an extendedheterologous transit peptide from C. protothecoides and a 41 aminoacid N-terminal extension derived from the native Cpal FATB2sequence in construct D1481 [pSZ2479]GCGCACCCCAAGGCGAACGGCAGCGCGGTGTCGCTGAAGTCGGGCTCCCIGGAGACCCAGGAGGACAAGACGAGCAGCTCGTCCCCCCCCCCCCGCACGTTCATCAACCAGCTGCCCGTGTGGAGCATGCTGCTGTCGGCGGTGACCACGGTCTTCGGCGTGGCCGAGAAGCAGTGGCCCATGCTGGACCGCAAGTCCAAGCGCCCCGACATGCTGGTCGAGCCCCTGGGCGTGGACCGCATCGTCTACGACGGCGTGAGCTTCCGCCAGTCGTTCTCCATCCGCAGCTACGAGATCGGCGCCGACCGCACCGCCTCGATCGAGACGCTGATGAACATGTTCCAGGAGACCTCCCTGAACCACTGCAAGATCATCGGCCTGCTGAACGACGGCTTCGGCCGCACGCCCGAGATGTGCAAGCGCGACCTGATCTGGGTCGTGACCAAGATGCAGATCGAGGTGAACCGCTACCCCACGTGGGGCGACACCATCGAGGTCAACACGTGGGTGAGCGCCTCGGGCAAGCACGGCATGGGCCGCGACTGGCTGATCTCCGACTGCCACACCGGCGAGATCCTGATCCGCGCGACGAGCGTCTGGGCGATGATGAACCAGAAGACCCGCCGCCTGTCGAAGATCCCCTACGAGGTGCGCCAGGAGATCGAGCCCCAGTTCGTCGACTCCGCCCCCGTGATCGTGGACGACCGCAAGTTCCACAAGCTGGACCTGAAGACGGGCGACAGCATCTGCAACGGCCTGACCCCCCGCTGGACGGACCTGGACGTGAACCAGCACGTCAACAACGTGAAGTACATCGGCTGGATCCTGCAGTCGGTCCCCACCGAGGTGTTCGAGACGCAGGAGCTGTGCGGCCTGACCCTGGAGTACCGCCGCGAGTGCGGCCGCGACTCCGTGCTGGAGAGCGTCACGGCCATGGACCCCTCGAAGGAGGGCGACCGCTCCCTGTACCAGCACCTGCTGCGCCTGGAGGACGGCGCGGACATCGTGAAGGGCCGCACCGAGTGGCGCCCCAAGAACGCCGGCGCCAAGGGCGCCATCCTGACGGGCAAGACCAGCAACGGCAACTCGATCTCCTGA SEQ ID NO: 87Amino acid sequence of 14:0-ACP thioesterase, Cuphea palustris (CpalFATB2, accession AAC49180) containing an extended heterologoustransit peptide from C. protothecoides and a 41 amino acid N-terminal extension derived from the native Cpal FATB2 sequenceencoded by construct D1481 [pSZ2479]AHPKANGSAVSLKSGSLETQEDKTSSSSPPPRTFINQLPVWSMLLSAVTTVFGVAEKQWPMLDRKSKRPDMLVEPLGVDRIVYDGVSFRQSFSIRSYEIGADRTASIETLMNMFQETSLNHCKIIGLLNDGFGRTPEMCKRDLIWVVTKMQIEVNRYPTWGDTIEVNTWVSASGKHGMGRDWLISDCHTGEILIRATSVMAMMNQKTRRLSKIPYEVRQEIEPQFVDSAPVIVDDRKFHKLDLKTGDSICNGLTPRWTDLDVNQHVNNVKYIGWILQSVPTEVFETQELCGLTLEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIVKGRTEWRPKNAGAKGAILTGKTSN GNSISSEQ ID No: 88Nucleic acid sequence encoding 14:0-ACP thioesterase, Cupheapalustris (Cpal FATB2, accession AAC49180) containing an extendedheterologous transit peptide from C. protothecoides, a 41 aminoacid N-terminal extension derived from the native Cpal FATB2sequence, and a C-terminal FLAG epitope tag in construct D1482 [pSZ2480]GCGCACCCCAAGGCGAACGGCAGCGCGGTGTCGCTGAAGTCGGGCTCCCTGGAGACCCAGGAGGACAAGACGAGCAGCTCGTCCCCCCCCCCCCGCACGTTCATCAACCAGCTGCCCGTGTGGAGCATGCTGCTGTCGGCGGTGACCACGGTCTTCGGCGTGGCCGAGAAGCAGTGGCCCATGCTGGACCGCAAGTCCAAGCGCCCCGACATGCTGGTCGAGCCCCTGGGCGTGGACCGCATCGTCTACGACGGCGTGAGCTTCCGCCAGTCGTTCTCCATCCGCAGCTACGAGATCGGCGCCGACCGCACCGCCTCGATCGAGACGCTGATGAACATGTTCCAGGAGACCTCCCTGAACCACTGCAAGATCATCGGCCTGCTGAACGACGGCTTCGGCCGCACGCCCGAGATGTGCAAGCGCGACCTGATCTGGGTCGTGACCAAGATGCAGATCGAGGTGAACCGCTACCCCACGTGGGGCGACACCATCGAGGTCAACACGTGGGTGAGCGCCTCGGGCAAGCACGGCATGGGCCGCGACTGGCTGATCTCCGACTGCCACACCGGCGAGATCCTGATCCGCGCGACGAGCGTCTGGGCGATGATGAACCAGAAGACCCGCCGCCTGTCGAAGATCCCCTACGAGGTGCGCCAGGAGATCGAGCCCCAGTTCGTCGACTCCGCCCCCGTGATCGTGGACGACCGCAAGTTCCACAAGCTGGACCTGAAGACGGGCGACAGCATCTGCAACGGCCTGACCCCCCGCTGGACGGACCTGGACGTGAACCAGCACGTCAACAACGTGAAGTACATCGGCTGGATCCTGCAGTCGGTCCCCACCGAGGTGTTCGAGACGCAGGAGCTGTGCGGCCTGACCCTGGAGTACCGCCGCGAGTGCGGCCGCGACTCCGTGCTGGAGAGCGTCACGGCCATGGACCCCTCGAAGGAGGGCGACCGCTCCCTGTACCAGCACCTGCTGCGCCTGGAGGACGGCGCGGACATCGTGAAGGGCCGCACCGAGTGGCGCCCCAAGAACGCCGGCGCCAAGGGCGCCATCCTGACGGGCAAGACCAGCAACGGCAACTCGATCTCCatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaagtga SEQ ID NO: 89Amino acid sequence of 14:0-ACP thioesterase, Cuphea palustris (CpalFATB2, accession AAC49180) containing an extended heterologoustransit peptide from C. protothecoides, a 41 amino acid N-terminalextension derived from the native Cpal FATB2 sequence, and a C-terminal FLAG epitope tag encoded by construct D1482 [pSZ2480]AHPKANGSAVSLKSGSLETQEDKTSSSSPPPRTFINQLPVWSMLLSAVTTVFGVAEKQWPMLDRKSKRPDMLVEPLGVDRIVYDGVSFRQSFSIRSYEIGADRTASIETLMNMFQETSLNHCKIIGLLNDGFGRTPEMCKRDLIWVVTKMQIEVNRYPTWGDTIEVNTWVSASGKHGMGRDWLISDCHTGEILIRATSVMAMMNQKTRRLSKIPYEVRQEIEPQFVDSAPVIVDDRKFHKLDLKTGDSICNGLTPRWTDLDVNQHVNNVKYIGWILQSVPTEVFETQELCGLTLEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIVKGRTEWRPKNAGAKGAILTGKTSNGNSISMDYKDHDGDYKDHDIDYKDDDDK SEQ ID NO: 154Cuphea hyssopifolia FATB3 coding region, codon optimized forPrototheca moriformisgtggccgccgaggcctcctccgccctgttctccgtgcgcacccccggcacctcccccaagcccggcaagttcggcaactggcccacctccctgtccgtgcccttcaagtccaagtccaaccacaacggcggcttccaggtgaaggccaacgcctccgcccgccccaaggccaacggctccgccgtgtccctgaagtccggctccctggacacccaggaggacacctcctcctcctcctcccccccccgcaccttcatcaaccagctgcccgactggtccatgctgctgtccgccatcaccaccgtgttcgtggccgccgagaagcagtggaccatgctggaccgcaagtccaagcgccccgacatgctgatggaccccttcggcgtggaccgcgtggtgcaggacggcgccgtgttccgccagtccttctccatccgctcctacgagatcggcgccgaccgcaccgcctccatcgagaccctgatgaacatcttccaggagacctccctgaaccactgcaagtccatcggcctgctgaacgacggcttcggccgcacccccgagatgtgcaagcgcgacctgatctgggtggtgaccaagatgcacgtggaggtgaaccgctaccccacctggggcgacaccatcgaggtgaacacctgggtgtccgagtccggcaagaccggcatgggccgcgactggctgatctccgactgccacaccggcgagatcctgatccgcgccacctccatgtgcgccatgatgaaccagaagacccgccgcttctccaagttcccctacgaggtgcgccaggagctggccccccacttcgtggactccgcccccgtgatcgaggactaccagaagctgcacaagctggacgtgaagaccggcgactccatctgcaacggcctgaccccccgctggaacgacctggacgtgaaccagcacgtgaacaacgtgaagtacatcggctggatcctggagtccgtgcccaccgaggtgttcgagacccaggagctgtgcggcctgaccctggagtaccgccgcgagtgcggccgcgactccgtgctggagtccgtgaccgccatggacccctccaaggagggcgaccgctccctgtaccagcacctgctgcgcctggaggacggcgccgacatcgccaagggccgcaccaagtggcgccccaagaacgccggcaccaacggcgccatctccaccggcaagacctccaacggcaactccatctccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag SEQ ID NO: 155Cuphea hyssopifolia FATB1 coding region, codon optimized forPrototheca moriformisgccaccgcctccaccttctccgccttcaacgcccgctgcggcgacctgcgccgctccgccggctccggcccccgccgccccgcccgccccctgcccgtgcgcgccgccatcaacgcctccgcccaccccaaggccaacggctccgccgtgaacctgaagtccggctccctggagacccaggaggacacctcctcctcctccccccoccoccgcaccttcatcaagcagctgcccgactggggcatgctgctgtccaagatcaccaccgtgttcggcgccgccgagcgccagtggaagcgcccoggcatgctggtggagccottoggcgtggaccgcatcttccaggacggcgtgttottccgccagtocttctccatccgctcctacgagatcggcgccgaccgcaccgcctccatcgagaccctgatgaacatcttccaggagacctocctgaaccactgcaagtccatcggcctgctgaacgacggcttoggccgcaccoccgagatgtgcaagcgcgacctgatctgggtggtgaccaagatccaggtggaggtgaaccgctaccccacctggggcgacaccatcgaggtgaacacctgggtgtccgagtcoggcaagaacggcatgggccgcgactggctgatctccgactgccgcaccggcgagatcctgatccgcgccacctccgtgtgggccatgatgaaccgcaagacccgccgcctgtccaagttccoctacgaggtgcgccaggagatcgccocccacttcgtggactccgccoccgtgatcgaggacgacaagaagctgcacaagctggacgtgaagaccggcgactccatccgcaagggcctgaccocccgctggaacgacctggacgtgaaccagcacgtgaacaacgtgaagtacatoggctggatcctgaagtccgtgcccgccgaggtgttcgagacccaggagctgtgoggcgtgaccctggagtaccgccgcgagtgoggccgcgactccgtgctggagtccgtgaccgccatggacaccgccaaggagggcgaccgctocctgtaccagcacctgctgcgcctggaggacggcgccgacatcaccatoggccgcaccgagtggcgccocaagaacgccggcgccaacggcgccatctccaccggcaagacctccaacgagaactccgtgtccatggactacaaggaccacgacggcgactacaaggaccacgacatcgactacaaggacgacgacgacaag SEQ ID NO: 156Garcinia mangostana FATA1 CDSMLKLSSSRSPLARIPTRPRPNSIPPRIIVVSSSSSKVNPLKTEAVVSSGLADRLRLGSLTEDGLSYKEKFIVRCYEVGINKTATVETIANLLQEVGCNHAQSVGYSIGGFSTIPTMRKLRLIWVTARMHIEIYKYPAWSDVVEIESWGQGEGKIGIRRDWILRDYATGQVIGRATSKWVMMNQDTRRLQKVDVDVRDEYLVHCPRELRLAFPEENNSSLKKISKLEDPSQYSKLGLVPRRADLDMNQHVNNVIYIGWVLESMPQEIIDTHELQIITLDYRRECQHDDVVDSLTSPEPSEDAEAVFNHNGINGSANVSANDHGCRNFLHLLRLSGNGLEINRGRIEWRKKPTR SEQ ID NO: 157 Brassic napus LPAAT CDSMAMAAAVIVPLGILFFISGLVVNLLQAVCYVLVRPMSKNTYRKINRVVAETLWLELVWIVDWWAGVKIQVFADDETFNRMGKEHALVVCNHRSDIDWLVGWILAQRSGCLGSALAVMKKSSKFLPVIGWSMWFSEYLFLERNWAKDESTLQSGLQRLNDFPRPFWLALFVEGTRFTEAKLKAAQEYAASSELPVPRNVLIPRIKGFVSAVSNMRSFVPAIYDMTVAIPKTSPPPTMLRLFKGQPSVVHVHIKCHSMKDLPEPEDEIAQWCRDQFVAKDALLDKHIAADTFPGQKEQNIGRPIKSLAVVVSWACLLTLGAMKFLHWSNLFSSWKGIALSAFGLGIITLCMQILIRSSQSERSTPAKVAPAKPKDNHQSGPSSQTEVEEKQK SEQ ID NO: 158Cuphea hookeriana FATB2 CDSMVAAAASSAFFPVPAPGASPKPGKEGNWPSSLSPSFKPKSIPNGGFQVKANDSAHPKANGSAVSLKSGSLNIQEDISSSPPPRTFLHQLPDWSRLLTAITIVFVKSKRPDMHDRKSKRPDMLVDSFGLESTVQDGLVFRQSFSIRSYEIGTDRTASIETLMNHLQETSLNHCKSTGILLDGFGRTLEMCKRDLIWVVIKMQIKVNRYPAWGDIVEINTRFSRLGKIGMGRDWLISDCNTGEILVRATSAYAMMNQKTRRLSKLPYEVHQEIVPLFVDSPVIEDSDLKVHKEKVKIGDSIQKGLIPGWNDLDVNQHVSNVKYIGWILESMPTEVLETQELCSLALEYRRECGRDSVLESVTAMDPSKVGVRSQYQHLLRLEDGTAIVNGATEWRPKNAGANGAISIGKISNGNSVSSEQ ID NO: 159Cuphea wrightii KASAI CDS with P moriformis SAD transit peptide(underlined)MASAAFTMSACPAMTGRAPGARRSGRPVATRLRYVFQCLVASCIDPCDQYRSSASLSFLGDNGFASLFGSKPFMSNRGHRRLRRASHSGEAMAVALQPAQEAGIKKKPVIKQRRVVVTGMGVVTPLGHEPDVFYNNLLDGVSGISEIETEDCTQFPTRIAGEIKSFSIDGWVAPKLSKRMDKFMLYLLTAGKKALADGGITDEVMKELDKRKCGVLIGSGMGGMKVFNDAIEALRVSYKKMNPFCVPFATTNMGSAMLAMDLGWMGPNYSISTACATSNFCILNAANHIIRGEADMMLCGGSDAVIIPIGLGGFVACRALSQRNSDPIKASRPWDSNRDGFVMGEGAGVLLLEELEHAKKRGATIYAEFLGGSFTCDAYHMTEPHPEGAGVILCIEKALAQAGVSKEDVNYINAHATSTSAGDIKEYQALARCFGQNSELRVNSTKSMIGHLLGAAGGVEAVTVVQAIRTGWIHPNLNLEDPDKAVDAKLLVGPKKERLNVKVGLSNSFGEGGHNSSILFAPCNV SEQ ID NO: 160Native Protheca moriformis KASII amino acid sequence (native transitpeptide is underlined)MQTAHQRPPTEGHCFGARLPTASRRAVRRAWSRIARAAAAADANPARPERRVVITGQGVVTSLGQTIEQFYSSLLEGVSGISQIQKFDTTGYTTTIAGEIKSLQLDPYVPKRWAKRVDDVIKYVYIAGKQALESAGLPIEAAGLAGAGLDPALCGVLIGTAMAGMTSFAAGVEALTRGGVRKMNPFCIPFSISNMGGAMLAMDIGFMGPNYSISTACAIGNYCILGAADHIRRGDANVMLAGGADAAIIPSGIGGFIACKALSKRNDEPERASRPWDADRDGFVMGEGAGVLVLEELEHAKRRGATILAELVGGAATSDAHHMTEPDPQGRGVRLCLERALERARLAPERVGYVNAHGTSTPAGDVAEYRAIRAVIPQDSLRINSTKSMIGHLLGGAGAVEAVAAIQALRTGWLHPNLNLENPAPGVDPVVLVGPRKERAEDLDVVLSNSFGEGGHNSCVIERKYDESEQ ID NO: 161Mature native Protheca moriformis KASII amino acid sequence (nativetransit peptide is underlined)AAAAADANPARPERRVVITGQGVVISLGQIIEQFYSSLLEGVSGISQIQKFDTTGYTTTIAGEIKSLQLDPYVPKRWAKRVDDVIKYVYIAGKQALESAGLPIEAAGLAGAGLDPALCGVLIGTAMAGMTSFAAGVEALTRGGVRKMNPFCIPFSISNMGGAMLAMDIGFMGPNYSISTACAIGNYCILGAADHIRRGDANVMLAGGADAAIIPSGIGGFIACKALSKRNDEPERASRPWDADRDGFVMGEGAGVLVLEELEHAKRRGATILAELVGGAATSDAHHMTEPDPQGRGVRLCLERALERARLAPERVGYVNAHGTSTPAGDVAEYRAIRAVIPQDSLRINSTKSMIGHLLGGAGAVEAVAAIQALRIGWLHPNLNLENPAPGVDPVVLVGPRKERAEDLDVVLSNSFGFGGHNSCVIFRKYDE SEQ ID NO: 162 CcFATB2-UcFATB2 chimeric FATBPDWSMLFAVITTIFSAAEKQWTNLEWKPKPNPPQLLDDHFGPHGLVERRTFAIRSYEVGPDRSTSIVAVMNHLQEAALNHAKSVGILGDGFGTTLEMSKRDLIWVVRRTHVAVERYPTWGDIVEVECWIGASGNNGMRRDFLVRDCKTGEILTRCTSLSVLMNTRIRRLSTIPDEVRGEIGPAFIDNVAVKDDEIKKLQKLNDSTADYIQGGLIPRWNDLDVNQHVNNLKYVAWVFETVPDSIFESHHISSFTLEYRRECTRDSVLRSLTTVSGGSSEAGLVCDHLLQLEGGSEVLRARTEWRPKLTDSFRGISVIPAEPRV SEQ ID NO: 163 Cuphea hyssopifolia FATB1MVATNAAAFSAYTFFLTSPTHGYSSKRLADTQNGYPGTSLKSKSTPPPAAAAARNGALPLLASICKCPKKADGSMQLDSSLVEGFQFYIRSYEVGADQTVSIQTVLNYLQEAAINHVQSAGYFGDSFGATPEMTKRNLIWVITKMQVLVDRYPAWGDVVQVDTWICSSGKNSMQRDWFVRDLKTGDIITRASSVWVLMNRLTRKLSKIPEAVLEEAKLFVMNTAPTVDDNRKLPKLDGSSADYVLSGLTPRWSDLDMNQHVNNVKYIAWILESVPQSIPETHKLSAITVEYRRECGKNSVLQSLTNVSGDGITCGNSIIECHHLLQLETGPEILLARTEWISKEPGFRGAPIQAEKVYNNK* SEQ ID NO: 164 Cuphea hyssopifolia FATB3MVAAEASSALFSVRTPGTSPKPGKFGNWPTSLSVPFKSKSNHNGGFQVKANASARPKANGSAVSLKSGSLDTQEDTSSSSSPPRTFINQLPDWSMLLSAITTVFVAAEKQWTMLDRKSKRPDMLMDPFGVDRVVQDGAVFRQSFSIRSYEIGADRTASIETLMNIFQETSLNHCKSIGLLNDGFGRTPEMCKRDLIWVVTKMHVEVNRYPTWGDTIEVNTWVSESGKTGMGRDWLISDCHTGEILIRATSMCAMMNQKTRRESKFPYEVRQELAPHFVDSAPVIEDYQKLHKLDVKTGDSICNGLTPRWNDLDVNQHVNNVKYIGWILESVPTEVFETQELCGLTLEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIAKGRTKWRPKNAGTNGAISTGKTSNGNSIS*

1.-84. (canceled)
 85. A recombinant cell of the genus Prototheca orChlorella, said recombinant cell comprising a knockout or knockdown ofan endogenous Fatty acyl-ACP thioesterase gene, and further comprisingexogenous nucleic acids that encode lysophosphatidic acidacyltransferase (LPAAT).
 86. The recombinant cell of claim 85, whereinsaid exogenous nucleic acids that encode LPAAT encodes an LPPAT havingat least 90% amino acid sequence identity to an LPAAT selected from thegroup consisting of SEQ ID NOs: 16, 77, 78, 79 and
 157. 87. Therecombinant cell of claim 86, wherein said exogenous nucleic acids thatencode LPAAT encodes an LPPAT having at least 95% amino acid sequenceidentity to an LPAAT selected from the group consisting of SEQ ID NOs:16, 77, 78, 79 and
 157. 88. The recombinant cell of claim of claim 86,wherein said exogenous nucleic acids encodes an LPAAT comprising theamino acid sequences of SEQ ID NO:
 157. 89. The recombinant cell ofclaim of claim 86, wherein said exogenous nucleic acids encodes an LPAATcomprising the amino acid sequences of SEQ ID NOs: 17, 77, 78 or
 79. 90.The recombinant cell of claim 89, wherein said exogenous nucleic acidsthat encode LPAAT are nucleic acids having at least 90% sequenceidentity to the nucleic acids selected from the group consisting of SEQID NOs: 18, 80, 81, 82, 83, 84 and
 85. 91. The recombinant cell of claim85, wherein said exogenous nucleic acids that encode LPAAT are nucleicacids having at least 95% sequence identity to the nucleic acidsselected from the group consisting of SEQ ID NOs: 18, 80, 81, 82, 83, 84and
 85. 92. The recombinant cell of claim 85, wherein triglyceride oilproduced by the recombinant cell is enriched in stearate-oleate-stearate(SOS) triglycerides.
 93. The recombinant cell of claim 92, wherein theSOS triglyceride content comprises at least 50% of the triglycerideoils.
 94. The recombinant cell of claim 93, wherein the SOS triglyceridecontent comprises at least 60% of the triglyceride oils.
 95. Therecombinant cell of claim 85, wherein triglyceride oil produced by therecombinant cell is enriched in mid-chain fatty acid.
 96. Therecombinant cell of claim 95, wherein the triglyceride oil is enrichedin C12:0.
 97. The method of claim 85, wherein said recombinant cell isof the genus Prototheca.
 98. The method of claim 97, wherein saidrecombinant cell is a Prototheca moriformis cell.
 99. The method ofclaim 92, wherein said recombinant cell is of the genus Prototheca. 100.The method of claim 99, wherein said recombinant cell is a Protothecamoriformis cell.
 101. A method of producing oil, the method comprisingthe steps of: a. cultivating a recombinant cell of the genus Protothecaor Chlorella, said recombinant cell comprising a knockout or knockdownof an endogenous Fatty acyl-ACP thioesterase gene, and furthercomprising exogenous nucleic acids that encode lysophosphatidic acidacyltransferase (LPAAT); and b. isolating the oil from said recombinantcell.
 102. The method of claim 101, wherein said recombinant cell is ofthe genus Prototheca.
 103. The method of claim 102, wherein saidrecombinant cell is a Prototheca moriformis cell.
 104. An oil producedby the steps of: a. cultivating a recombinant cell of the genusPrototheca or Chlorella, said recombinant cell comprising a knockout orknockdown of an endogenous Fatty acyl-ACP thioesterase gene, and furthercomprising exogenous nucleic acids that encode lysophosphatidic acidacyltransferase (LPAAT); and b. isolating the oil from said recombinantcell.